1 Introduction

1.1 Motivation

The spatialHeatmap package provides functionalities for visualizing cell-, tissue- and organ-specific data of biological assays by coloring the corresponding spatial features defined in anatomical images according to a numeric color key. The color scheme used to represent the assay values can be customized by the user. This core functionality of the package is called a spatial heatmap (SHM) plot. It is enhanced with visualization tools for groups of measured items (e.g. gene modules) sharing related abundance profiles, including matrix heatmaps combined with hierarchical clustering dendrograms and network representations. The functionalities of spatialHeatmap can be used either in a command-driven mode from within R or a graphical user interface (GUI) provided by a Shiny App that is also part of this package. While the R-based mode provides flexibility to customize and automate analysis routines, the Shiny App includes a variety of convenience features that will appeal to experimentalists and other users less familiar with R. Moreover, the Shiny App can be used on both local computers as well as centralized server-based deployments (e.g. cloud-based or custom servers) that can be accessed remotely as a public web service for using spatialHeatmap’s functionalities with community and/or private data. The functionalities of the spatialHeatmap package are illustrated in Figure 1.

Overview of spatialHeatmap. (A) The _saptialHeatmap_ package plots numeric assay data onto spatially annotated images. A wide range of omics technologies is supported including genomic, transcriptomic, proteomic and metabolomic profiling data. The assay data can be provided as numeric vectors, tabular data, or _SummarizedExperiment_ objects. The latter is a widely used data container for organizing both assay data as well as associated annotation and experimental design data. (B) Anatomical and other spatial images need to be provided as annotated SVG (aSVG) files where the spatial features and the corresponding data components of the assay data have matching labels (_e.g._ tissue labels). (C) The assay data are used to color the matching spatial features in one or more aSVG images according to a color key. The result is called a spatial heatmap (SHM) or spatiotemporal heatmap (STHM) plot. Multiple measurements can be visualized in the same plot, such as several factors (_e.g._ genes, proteins, metabolites), treatment conditions, growth stages and more. (D) Data mining graphics, such as matrix heatmaps and network graphs, are integrated to facilitate the identification of factors with similar assay profiles. The functionalities of _spatialHeatmap_ can be accessed from local computers via the R console or a graphical user interface based on Shiny. In addition, the latter can be deployed as a web service on custom servers or cloud-based systems.

Figure 1: Overview of spatialHeatmap
(A) The saptialHeatmap package plots numeric assay data onto spatially annotated images. A wide range of omics technologies is supported including genomic, transcriptomic, proteomic and metabolomic profiling data. The assay data can be provided as numeric vectors, tabular data, or SummarizedExperiment objects. The latter is a widely used data container for organizing both assay data as well as associated annotation and experimental design data. (B) Anatomical and other spatial images need to be provided as annotated SVG (aSVG) files where the spatial features and the corresponding data components of the assay data have matching labels (e.g. tissue labels). (C) The assay data are used to color the matching spatial features in one or more aSVG images according to a color key. The result is called a spatial heatmap (SHM) or spatiotemporal heatmap (STHM) plot. Multiple measurements can be visualized in the same plot, such as several factors (e.g. genes, proteins, metabolites), treatment conditions, growth stages and more. (D) Data mining graphics, such as matrix heatmaps and network graphs, are integrated to facilitate the identification of factors with similar assay profiles. The functionalities of spatialHeatmap can be accessed from local computers via the R console or a graphical user interface based on Shiny. In addition, the latter can be deployed as a web service on custom servers or cloud-based systems.

As anatomical images the package supports both tissue maps from public repositories and custom images provided by the user. In general any type of image can be used as long as it can be provided in SVG (Scalable Vector Graphics) format, where the corresponding spatial features have been defined (see aSVG below). The numeric values plotted onto an SHM are usually quantitative measurements from a wide range of profiling technologies, such as microarrays, next generation sequencing (e.g. RNA-Seq and scRNA-Seq), proteomics, metabolomics, or many other small- or large-scale experiments. For convenience, several preprocessing and normalization methods for the most common use cases are included that support raw and/or preprocessed data. Currently, the main application domains of the spatialHeatmap package are numeric data sets and spatially mapped images from biological, agricultural and biomedical areas. Moreover, the package has been designed to also work with many other spatial data types, such a population data plotted onto geographic maps. This high level of flexibility is one of the unique features of spatialHeatmap. Related software tools for biological applications in this field are largely based on pure web applications (Lekschas et al. 2015; Papatheodorou et al. 2018; Winter et al. 2007; Waese et al. 2017) or local tools (Maag 2018; Muschelli, Sweeney, and Crainiceanu 2014) that typically lack customization functionalities. These restrictions limit users to utilizing pre-existing expression data and/or fixed sets of anatomical image collections. To close this gap for biological use cases, we have developed spatialHeatmap as a generic R/Bioconductor package for plotting quantitative values onto any type of spatially mapped images in a programmable environment and/or in an intuitive to use GUI application.

1.2 Design

The core feature of spatialHeatmap is to map assay values (e.g. gene expression data) of one or many items (e.g. genes) measured under different conditions in form of numerically graded colors onto the corresponding cell types or tissues represented in a chosen SVG image. In the gene profiling field, this feature supports comparisons of the expression values among multiple genes by plotting their SHMs next to each other. Similarly, one can display the expression values of a single or multiple genes across multiple conditions in the same plot (Figure 4). This level of flexibility is very efficient for visualizing complicated expression patterns across genes, cell types and conditions. In case of more complex anatomical images with overlapping multiple layer tissues, it is important to visually expose the tissue layer of interest in the plots. To address this, several default and customizable layer viewing options are provided. They allow to hide features in the top layers by making them transparent in order to expose features below them. This transparency viewing feature is highlighted below in the mouse example (Figure 5). Except for spatial data, this package also works on spatiotemporal data and generates spatiotemporal heatmaps (STHMs, Figure 9). Moreover, one can plot multiple distinct aSVGs in a single SHM plot as shown in Figure 11. This is particularly useful for displaying abundance trends across multiple development stages, where each is represented by its own aSVG image. In addition to static SHM representations, one can visualize them in form of dynamic animations embedded in interactive HTML files or generate videos for them.

To maximize reusability and extensibility, the package organizes large-scale omics assay data along with the associated experimental design information in a SummarizedExperiment object (Figure 1A). The latter is one of the core S4 classes within the Bioconductor ecosystem that has been widely adapted by many other software packages dealing with gene-, protein- and metabolite-level profiling data (Morgan et al. 2018). In case of gene expression data, the assays slot of the SummarizedExperiment container is populated with a gene expression matrix, where the rows and columns represent the genes and tissue/conditions, respectively, while the colData slot contains sample data including replicate information. The tissues and/or cell type information in the object maps via colData to the corresponding features in the SVG images using unique identifiers for the spatial features (e.g. tissues or cell types). This allows to color the features of interest in an SVG image according to the numeric data stored in a SummarizedExperiment object. For simplicity the numeric data can also be provided as numeric vectors or data.frames. This can be useful for testing purposes and/or the usage of simple data sets that may not require the more advanced features of the SummarizedExperiment class, such as measurements with only one or a few data points. The details about how to access the SVG images and properly format the associated expression data are provided in the Supplementary Section of this vignette.

1.3 Image Format: SVG

SHMs are images where colors encode numeric values in features of any shape. For plotting SHMs, Scalable Vector Graphics (SVG) has been chosen as image format since it is a flexible and widely adapted vector graphics format that provides many advantages for computationally embedding numerical and other information in images. SVG is based on XML formatted text describing all components present in images, including lines, shapes and colors. In case of biological images suitable for SHMs, the shapes often represent anatomical or cell structures. To assign colors to specific features in SHMs, annotated SVG (aSVG) files are used where the shapes of interest are labeled according to certain conventions so that they can be addressed and colored programmatically. SVGs and aSVGs of anatomical structures can be downloaded from many sources including the repositories described below. Alternatively, users can generate them themselves with vector graphics software such as Inkscape. Typically, in aSVGs one or more shapes of a feature of interest, such as the cell shapes of an organ, are grouped together by a common feature identifier. Via these group identifiers one or many feature types can be colored simultaneously in an aSVG according to biological experiments assaying the corresponding feature types with the required spatial resolution. Correct assignment of image features and assay results is assured by using for both the same feature identifiers. The color gradient used to visually represent the numeric assay values is controlled by a color gradient parameter. To visually interpret the meaning of the colors, the corresponding color key is included in the SHM plots. Additional details for properly formatting and annotating both aSVG images and assay data are provided in the Supplementary Section section of this vignette.

1.4 Data Repositories

If not generated by the user, SHMs can be generated with data downloaded from various public repositories. This includes gene, protein and metabolic profiling data from databases, such as GEO, BAR and Expression Atlas from EMBL-EBI (Papatheodorou et al. 2018). A particularly useful resource, when working with spatialHeatmap, is the EBI Expression Atlas. This online service contains both assay and anatomical images. Its assay data include mRNA and protein profiling experiments for different species, tissues and conditions. The corresponding anatomical image collections are also provided for a wide range of species including animals and plants. In spatialHeatmap several import functions are provided to work with the expression and aSVG repository from the Expression Atlas directly. The aSVG images developed by the spatialHeatmap project are available in its own repository called spatialHeatmap aSVG Repository, where users can contribute their aSVG images that are formatted according to our guidlines.

1.5 Tutorial Overview

The following sections of this vignette showcase the most important functionalities of the spatialHeatmap package using as initial example a simple to understand toy data set, and then more complex mRNA profiling data from the Expression Atlas and GEO databases. First, SHM plots are generated for both the toy and mRNA expression data. The latter include gene expression data sets from RNA-Seq and microarray experiments of Human Brain, Mouse Organs, Chicken Organs, and Arabidopsis Shoots. The first three are RNA-Seq data from the Expression Atlas, while the last one is a microarray data set from GEO. Second, gene context analysis tools are introduced, which facilitate the visualization of gene modules sharing similar expression patterns. This includes the visualization of hierarchical clustering results with traditional matrix heatmaps (Matrix Heatmap) as well co-expression network plots (Network). Third, an overview of the corresponding Shiny App is presented that provides access to the same functionalities as the R functions, but executes them in an interactive GUI environment (Chang et al., n.d.; Chang and Borges Ribeiro 2018). Fourth, more advanced features for plotting customized SHMs are covered using the Human Brain data set as an example.

2 Getting Started

2.1 Installation

The spatialHeatmap package should be installed from an R (version \(\ge\) 3.6) session with the BiocManager::install command.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("spatialHeatmap")

2.2 Packages and Documentation

Next, the packages required for running the sample code in this vignette need to be loaded.

library(spatialHeatmap); library(SummarizedExperiment); library(ExpressionAtlas); library(GEOquery)

The following lists the vignette(s) of this package in an HTML browser. Clicking the corresponding name will open this vignette.

browseVignettes('spatialHeatmap')

3 Spatial Heatmaps (SHMs)

3.1 Toy Example

SHMs are plotted with the spatial_hm function. To provide a quick and intuitive overview how these plots are generated, the following uses a generalized toy example where a small vector of random numeric values is generated that are used to color features in an aSVG image. The image chosen for this example is an aSVG depicting the human brain. The corresponding image file ‘homo_sapiens.brain.svg’ is included in this package for testing purposes. The path to this image on a user's system, where spatialHeatmap is installed, can be obtained with the system.file function.

3.1.1 aSVG Image

The following commands obtain the directory of the aSVG collection and the full path to the chosen target aSVG image on a user’s system, respectively.

svg.dir <- system.file("extdata/shinyApp/example", package="spatialHeatmap")
svg.hum <- system.file("extdata/shinyApp/example", 'homo_sapiens.brain.svg', package="spatialHeatmap")

To identify feature labels of interest in annotated aSVG images, the return_feature function can be used. The following searches the aSVG images stored in dir for the query terms ‘lobe’ and ‘homo sapiens’ under the feature and species fields, respectively. The identified matches are returned as a data.frame.

feature.df <- return_feature(feature=c('lobe'), species=c('homo sapiens'), remote=FALSE, dir=svg.dir)
## Accessing features... 
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0000451 LAYER_EFO 
## 
## homo.sapiens_brain.shiny_shm.svg, Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0001873 UBERON_0001872 UBERON_0002038 UBERON_0001874 UBERON_0001875 UBERON_0002360 
## 
## Duplicated title text detected: hippocampus 
## homo_sapiens.brain.svg,
feature.df
##          feature     stroke color             id element    parent order
## 1 occipital.lobe 0.08000000  none UBERON_0002021    path LAYER_EFO     3
## 2  parietal.lobe 0.08000000  none UBERON_0001872       g LAYER_EFO     4
## 3  temporal.lobe 0.08000000  none UBERON_0001871    path LAYER_EFO     8
## 4 occipital.lobe 0.01600000  none UBERON_0002021    path LAYER_EFO     7
## 5  parietal.lobe 0.07060588  none UBERON_0001872       g LAYER_EFO     8
## 6  temporal.lobe 0.01600000  none UBERON_0001871    path LAYER_EFO    24
##                                SVG
## 1 homo.sapiens_brain.shiny_shm.svg
## 2 homo.sapiens_brain.shiny_shm.svg
## 3 homo.sapiens_brain.shiny_shm.svg
## 4           homo_sapiens.brain.svg
## 5           homo_sapiens.brain.svg
## 6           homo_sapiens.brain.svg
fnames <- feature.df[, 1]

3.1.2 Numeric Data

The following example generates a small numeric toy vector, where the data slot contains four numbers and its name slot is populated with the three feature names obtained from the above aSVG image. In addition, a non-matching entry (here ‘notMapped’) is included for demonstration purposes. Note, the numbers are mapped to features via matching names among the numeric vector and the aSVG, respectively. Accordingly, only numbers and features with matching name counterparts can be colored in the aSVG image. Entries without name matches are indicated by a message printed to the R console, here “notMapped”. This behavior can be turned off with verbose=FALSE in the corresponding function call. In addition, a summary of the numeric assay to feature mappings is stored in the result data.frame returned by the spatial_hm function (see below).

my_vec <- sample(1:100, length(unique(fnames))+1)
names(my_vec) <- c(unique(fnames), 'notMapped')
my_vec
## occipital.lobe  parietal.lobe  temporal.lobe      notMapped 
##             60             77             66             56

3.1.3 Plot SHM

Next, the SHM is plotted with the spatial_hm function (Figure 2). Internally, the numbers in my_vec are translated into colors based on the color key assigned to the col.com argument, and then painted onto the corresponding features in the aSVG, where the path to the image file is defined by svg.path=svg.hum. The remaining arguments used here include: ID for defining the title of the plot; ncol for setting the column-wise layout of the plot excluding the feature legend plot on the right; and height for defining the height of the SHM relative to its width. In addition, the outline feature g4320 covers all tissue features due to its default color, so it is set transparent through ft.trans. More details of the transparency function is explained in the mouse example (Figure 5). In the given example (Figure 2) only three features in my_vec (‘occipital lobe’, ‘parietal lobe’, and ‘temporal lobe’) have matching entries in the corresponding aSVG.

shm.lis <- spatial_hm(svg.path=svg.hum, data=my_vec, ID='toy', ncol=1, height=0.9, width=0.8, sub.title.size=20, legend.nrow=2, ft.trans=c('g4320'))
## Coordinates: homo_sapiens.brain.svg ... 
## CPU cores: 1 
## Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0001873 UBERON_0001872 UBERON_0002038 UBERON_0001874 UBERON_0001875 UBERON_0002360 
## 
## Duplicated title text detected: hippocampus 
## Features in data not mapped: notMapped 
## ggplots/grobs: homo_sapiens.brain.svg ... 
## ggplot: toy, con  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## toy_con_1
SHM of human brain with toy data. The plots from left to right represent: color key, SHM and legend. The colors in the first two plots depict the user provided numeric values, whereas in the legend plot they are used to map the feature labels to the corresponding spatial regions in the image.

Figure 2: SHM of human brain with toy data
The plots from left to right represent: color key, SHM and legend. The colors in the first two plots depict the user provided numeric values, whereas in the legend plot they are used to map the feature labels to the corresponding spatial regions in the image.

The named numeric values in my_vec, that have name matches with the features in the chosen aSVG, are stored in the mapped_feature slot. The attributes of features are stored in feature_attribute slot.

# The SHM, mapped features, and feature attributes are stored in a list
names(shm.lis)
## [1] "spatial_heatmap"   "mapped_feature"    "feature_attribute"
# Mapped features
shm.lis[['mapped_feature']]
##   rowID     featureSVG value                    SVG
## 1   toy occipital.lobe    60 homo_sapiens.brain.svg
## 2   toy  parietal.lobe    77 homo_sapiens.brain.svg
## 3   toy  temporal.lobe    66 homo_sapiens.brain.svg
# Feature attributes
shm.lis[['feature_attribute']][1:3, ]
##          feature stroke color             id element        parent order
## 1          g4320  0.080  none          g4320       g LAYER_OUTLINE     1
## 2 locus.ceruleus  0.016  none UBERON_0002148    path     LAYER_EFO     1
## 3   diencephalon  0.016  none UBERON_0001894    path     LAYER_EFO     2
##                      SVG
## 1 homo_sapiens.brain.svg
## 2 homo_sapiens.brain.svg
## 3 homo_sapiens.brain.svg

3.2 Human Brain

This subsection introduces how to find cell- and tissue-specific assay data in the Expression Atlas database. After choosing a gene expression experiment, the data is downloaded directly into a user's R session. Subsequently, the expression values for selected genes can be plotted onto a chosen aSVG image with or without prior preprocessing steps (e.g. normalization). For querying and downloading expression data from the Expression Atlas database, functions from the ExpressionAtlas package are used (Keays 2019).

3.2.1 Gene Expression Data

The following example searches the Expression Atlas for expression data derived from specific tissues and species of interest, here ‘cerebellum’ and ‘Homo sapiens’, respectively.

To avoid repetitive downloading, the downloaded data sets are cached in ~/.cache/shm in all the following examples.

cache.pa <- '~/.cache/shm' # The path of cache.
all.hum <- read_cache(cache.pa, 'all.hum') # Retrieve data from cache.
if (is.null(all.hum)) { # Save downloaded data to cache if it is not cached.
  all.hum <- searchAtlasExperiments(properties="cerebellum", species="Homo sapiens")
  save_cache(dir=cache.pa, overwrite=TRUE, all.hum)
}

The search result is stored in a DFrame containing 13 accessions matching the above query. For the following sample code, the accession ‘E-GEOD-67196’ from Prudencio et al. (2015) has been chosen, which corresponds to an RNA-Seq profiling experiment of ‘cerebellum’ and ‘frontal cortex’ brain tissue from patients with amyotrophic lateral sclerosis (ALS). Details about the corresponding record can be returned as follows.

all.hum[2, ]
## DataFrame with 1 row and 4 columns
##     Accession      Species                  Type                  Title
##   <character>  <character>           <character>            <character>
## 1 E-MTAB-3358 Homo sapiens RNA-seq of coding RNA RNA-Seq CAGE (Cap An..

The getAtlasData function allows to download the chosen RNA-Seq experiment from the Expression Atlas and import it into a RangedSummarizedExperiment object of a user's R session.

rse.hum <- read_cache(cache.pa, 'rse.hum') # Read data from cache.
if (is.null(rse.hum)) { # Save downloaded data to cache if it is not cached.
  rse.hum <- getAtlasData('E-GEOD-67196')[[1]][[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, rse.hum)
}

The design of the downloaded RNA-Seq experiment is described in the colData slot of rse.hum. The following returns only its first five rows and columns.

colData(rse.hum)[1:5, 1:5]
## DataFrame with 5 rows and 5 columns
##            AtlasAssayGroup     organism   individual  organism_part
##                <character>  <character>  <character>    <character>
## SRR1927019              g1 Homo sapiens  individual1     cerebellum
## SRR1927020              g2 Homo sapiens  individual1 frontal cortex
## SRR1927021              g1 Homo sapiens  individual2     cerebellum
## SRR1927022              g2 Homo sapiens  individual2 frontal cortex
## SRR1927023              g1 Homo sapiens individual34     cerebellum
##                           disease
##                       <character>
## SRR1927019 amyotrophic lateral ..
## SRR1927020 amyotrophic lateral ..
## SRR1927021 amyotrophic lateral ..
## SRR1927022 amyotrophic lateral ..
## SRR1927023 amyotrophic lateral ..

3.2.2 aSVG Image

The following example shows how to download from the above described SVG repositories an aSVG image that matches the tissues and species assayed in the gene expression data set downloaded in the previous subsection. The return_feature function queries the repository for feature- and species-related keywords, here c('frontal cortex', 'cerebellum') and c('homo sapiens', 'brain'), respectively. To return matching aSVGs, the argument keywords.any is set to TRUE by default. When return.all=FALSE, only aSVGs matching the query keywords are returned and saved under dir. Otherwise, all aSVGs are returned regardless of the keywords. To avoid overwriting of existing SVG files, it is recommended to start with an empty target directory, here tmp.dir. To search a local directory for matching aSVG images, the argument setting remote=FALSE needs to be used, while specifying the path of the corresponding directory under dir. All or only matching features are returned if match.only is set to FALSE or TRUE, respectively.

tmp.dir <- paste0(normalizePath(tempdir(check=TRUE), winslash="/", mustWork=FALSE), '/shm')  # Create empty directory
feature.df <- return_feature(feature=c('frontal cortex', 'cerebellum'), species=c('homo sapiens', 'brain'), keywords.any=TRUE, return.all=FALSE, dir=tmp.dir, remote=TRUE, match.only=TRUE, desc=FALSE) # Query aSVGs
feature.df[1:8, ] # Return first 8 rows for checking
unique(feature.df$SVG) # Return all matching aSVGs

To build this vignettes according to the R/Bioconductor package requirements, the following code section uses the aSVG file instance included in the spatialHeatmap package rather than the downloaded instance from the previous example.

feature.df <- return_feature(feature=c('frontal cortex', 'cerebellum'), species=c('homo sapiens', 'brain'), keywords.any=TRUE, return.all=FALSE, dir=svg.dir, remote=FALSE)
## Accessing features... 
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0000451 LAYER_EFO 
## 
## homo.sapiens_brain.shiny_shm.svg, Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0001873 UBERON_0001872 UBERON_0002038 UBERON_0001874 UBERON_0001875 UBERON_0002360 
## 
## Duplicated title text detected: hippocampus 
## homo_sapiens.brain.svg,

Note, the target tissues frontal cortex and cerebellum are included in both the experimental design slot of the downloaded expression data as well as the annotations of the aSVG. This way these features can be colored in the downstream SHM plots. If necessary users can also change from within R the feature identifiers and names in an aSVG. Details on this utility are provided in the Supplementary Section.

feature.df
##                 feature     stroke color             id element    parent order
## 1  middle.frontal.gyrus 0.08000000  none UBERON_0002702    path LAYER_EFO     2
## 2     prefrontal.cortex 0.08230311  none UBERON_0000451       g LAYER_EFO     5
## 3        frontal.cortex 0.08000000  none UBERON_0001870    path LAYER_EFO     6
## 4       cerebral.cortex 0.08000000  none UBERON_0000956       g LAYER_EFO     7
## 5            cerebellum 0.08000000  none UBERON_0002037       g LAYER_EFO     9
## 6  middle.frontal.gyrus 0.01600000  none UBERON_0002702    path LAYER_EFO     6
## 7      cingulate.cortex 0.01600000  none UBERON_0003027    path LAYER_EFO    19
## 8     prefrontal.cortex 0.01600000  none UBERON_0000451       g LAYER_EFO    21
## 9        frontal.cortex 0.01600000  none UBERON_0001870    path LAYER_EFO    22
## 10      cerebral.cortex 0.01600000  none UBERON_0000956       g LAYER_EFO    23
## 11           cerebellum 0.01600000  none UBERON_0002037       g LAYER_EFO    25
##                                 SVG
## 1  homo.sapiens_brain.shiny_shm.svg
## 2  homo.sapiens_brain.shiny_shm.svg
## 3  homo.sapiens_brain.shiny_shm.svg
## 4  homo.sapiens_brain.shiny_shm.svg
## 5  homo.sapiens_brain.shiny_shm.svg
## 6            homo_sapiens.brain.svg
## 7            homo_sapiens.brain.svg
## 8            homo_sapiens.brain.svg
## 9            homo_sapiens.brain.svg
## 10           homo_sapiens.brain.svg
## 11           homo_sapiens.brain.svg

Since the Expression Atlas supports the cross-species anatomy ontology, the corresponding UBERON identifiers are included in the id column of the data.frame returned by the above function call of return_feature (Mungall et al. 2012). This ontology is also supported by the rols Bioconductor package (Gatto 2019).

3.2.3 Experimental Design

For organizing experimental designs and downstream plotting purposes, it can be desirable to customize the text in certain columns of colData. This way one can use the source data for displaying ‘pretty’ sample names in columns and legends of all downstream tables and plots, respectively, in a consistent and automated manner. To achieve this, the following example imports a ‘targets’ file that can be generated and edited by the user in a text or spreadsheet program. In the following example the target file content is used to replace the text in the colData slot of the RangedSummarizedExperiment object with a version containing shorter sample names that are more suitable for plotting purposes.

The following imports a custom target file containing simplified sample labels and experimental design information.

hum.tar <- system.file('extdata/shinyApp/example/target_human.txt', package='spatialHeatmap')
target.hum <- read.table(hum.tar, header=TRUE, row.names=1, sep='\t')

Load custom target data into colData slot.

colData(rse.hum) <- DataFrame(target.hum)

A slice of the simplified colData object is shown below, where the disease column contains now shorter labels than in the original data set. Additional details for generating and using target files in spatialHeatmap are provided in the Supplementary Section of this vignette.

colData(rse.hum)[c(1:3, 41:42), 4:5]
## DataFrame with 5 rows and 2 columns
##             organism_part     disease
##               <character> <character>
## SRR1927019     cerebellum         ALS
## SRR1927020 frontal cortex         ALS
## SRR1927021     cerebellum         ALS
## SRR1927059     cerebellum      normal
## SRR1927060 frontal cortex      normal

3.2.4 Preprocess Assay Data

The actual gene expression data of the downloaded RNA-Seq experiment is stored in the assay slot of rse.hum. Since it contains raw count data, it can be desirable to apply basic preprocessing routines prior to plotting spatial heatmaps. The following shows how to normalize the count data, aggregate replicates and then remove genes with unreliable expression responses. These preprocessing steps are optional and can be skipped if needed. For this, the expression data can be provided to the spatial_hm function directly, where it is important to assign to the sam.factor and con.factor arguments the corresponding sample and condition column names (Table 2).

For normalizing raw count data from RNA-Seq experiments, the norm_data function can be used. It supports the following pre-existing functions from widely used packages for analyzing count data in the next generation sequencing (NGS) field: calcNormFactors (CNF) from edgeR (Robinson, McCarthy, and Smyth 2010); as well as estimateSizeFactors (ESF), varianceStabilizingTransformation (VST), and rlog from DESeq2 (Love, Huber, and Anders 2014). The argument norm.fun specifies one of the four internal normalizing methods: CNF, ESF, VST, and rlog. If norm.fun='none', no normalization is applied. The arguments for each normalizing function are provided via a parameter.list, which is a list with named slots. For example, norm.fun='ESF' and parameter.list=list(type='ratio') is equivalent to estimateSizeFactors(object, type='ratio'). If paramter.list=NULL, the default arguments are used by the normalizing function assigned to norm.fun. For additional details, users want to consult the help file of the norm_data function by typing ?norm_data in the R console.

The following example uses the ESF normalization option. This method has been chosen mainly due to its good time performance.

se.nor.hum <- norm_data(data=rse.hum, norm.fun='ESF', log2.trans=TRUE)
## Normalising: ESF 
##    type 
## "ratio"

Replicates are aggregated with the aggr_rep function, where the summary statistics can be chosen under the aggr argument (e.g. aggr='mean'). The columns specifying replicates can be assigned to the sam.factor and con.factor arguments corresponding to samples and conditions, respectively. For tracking, the corresponding sample/condition labels are used as column titles in the aggregated assay instance, where they are concatenated with a double underscore as separator. In addition, the corresponding rows in the colData slot are collapsed accordingly.

se.aggr.hum <- aggr_rep(data=se.nor.hum, sam.factor='organism_part', con.factor='disease', aggr='mean')
## Syntactically valid column names are made!
assay(se.aggr.hum)[1:3, ]
##                 cerebellum__ALS frontal.cortex__ALS cerebellum__normal
## ENSG00000000003        7.024054            7.091484           6.406157
## ENSG00000000005        0.000000            1.540214           0.000000
## ENSG00000000419        7.866582            8.002549           8.073264
##                 frontal.cortex__normal
## ENSG00000000003               7.004446
## ENSG00000000005               1.403110
## ENSG00000000419               7.955709

To remove unreliable expression measures, filtering can be applied. The following example retains genes with expression values larger than 5 (log2 space) in at least 1% of all samples (pOA=c(0.01, 5)), and a coefficient of variance (CV) between 0.30 and 100 (CV=c(0.30, 100)).

se.fil.hum <- filter_data(data=se.aggr.hum, sam.factor='organism_part', con.factor='disease', pOA=c(0.01, 5), CV=c(0.3, 100), dir=NULL)
## Syntactically valid column names are made! 
## All values before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   0.000   0.287   2.442   4.268  19.991 
## All coefficient of variances (CVs) before filtering:
##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
## 0.0007742 0.0767696 0.4019655 0.6217813 0.9956157 2.0000000 
## All values after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   2.654   4.976   4.779   6.451  14.695 
## All coefficient of variances (CVs) after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.3001  0.3648  0.4637  0.5651  0.7392  1.1548

To inspect the results, the following returns three selected rows of the fully preprocessed data matrix (Table 1).

assay(se.fil.hum)[c(5, 733:734), ]

Table 1: Slice of fully preprocessed expression matrix.
cerebellum__ALS frontal.cortex__ALS cerebellum__normal frontal.cortex__normal
ENSG00000006047 1.134172 5.2629629 0.5377534 5.3588310
ENSG00000268433 5.324064 0.3419665 3.4780744 0.1340332
ENSG00000268555 5.954572 2.6148548 4.9349736 2.0351776

3.2.5 SHM: Single Gene

The preprocessed expression values for any gene in the assay slot of se.fil.hum can be plotted as an SHM. The following uses gene ENSG00000268433 as an example. The chosen aSVG is a depiction of the human brain where the assayed featured are colored by the corresponding expression values in se.fil.hum.

shm.lis <- spatial_hm(svg.path=svg.hum, data=se.fil.hum, ID=c('ENSG00000268433'), height=0.7, legend.r=1.5, legend.key.size=0.02, legend.text.size=12, legend.nrow=2, ft.trans=c('g4320'))
## Coordinates: homo_sapiens.brain.svg ... 
## CPU cores: 1 
## Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0001873 UBERON_0001872 UBERON_0002038 UBERON_0001874 UBERON_0001875 UBERON_0002360 
## 
## Duplicated title text detected: hippocampus 
## ggplots/grobs: homo_sapiens.brain.svg ... 
## ggplot: ENSG00000268433, ALS  normal  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## ENSG00000268433_ALS_1  ENSG00000268433_normal_1
SHM of human brain. Only cerebellum and frontal cortex are colored, because they are present in both the aSVG and the expression data. The legend plot on the right maps the feature labels to the corresponding spatial regions in the image.

Figure 3: SHM of human brain
Only cerebellum and frontal cortex are colored, because they are present in both the aSVG and the expression data. The legend plot on the right maps the feature labels to the corresponding spatial regions in the image.

The plotting instructions of the SHM along with the corresponding mapped features and feature attributes are stored as a list, here named shm.lis. Its components can be accessed as follows.

names(shm.lis) # All slots.
## [1] "spatial_heatmap"   "mapped_feature"    "feature_attribute"
shm.lis[['mapped_feature']] # Mapped features.
##             rowID     featureSVG condition     value                    SVG
## 1 ENSG00000268433     cerebellum       ALS 5.3240638 homo_sapiens.brain.svg
## 2 ENSG00000268433 frontal.cortex       ALS 0.3419665 homo_sapiens.brain.svg
## 3 ENSG00000268433     cerebellum    normal 3.4780744 homo_sapiens.brain.svg
## 4 ENSG00000268433 frontal.cortex    normal 0.1340332 homo_sapiens.brain.svg
shm.lis[['feature_attribute']][1:3, ] # Feature attributes.
##          feature stroke color             id element        parent order
## 1          g4320  0.080  none          g4320       g LAYER_OUTLINE     1
## 2 locus.ceruleus  0.016  none UBERON_0002148    path     LAYER_EFO     1
## 3   diencephalon  0.016  none UBERON_0001894    path     LAYER_EFO     2
##                      SVG
## 1 homo_sapiens.brain.svg
## 2 homo_sapiens.brain.svg
## 3 homo_sapiens.brain.svg

In the above example, the normalized expression values of gene ENSG00000268433 are colored in the frontal cortex and cerebellum, where the different conditions, here normal and ALS, are given in separate SHMs plotted next to each other. The color and feature mappings are defined by the corresponding color key and legend plot on the left and right, respectively.

3.2.6 SHM: Multiple Genes

SHMs for multiple genes can be plotted by providing the corresponding gene IDs under the ID argument as a character vector. The spatial_hm function will then sequentially arrange the SHMs for each gene in a single composite plot. To facilitate comparisons among expression values across genes and/or conditions, the lay.shm parameter can be assigned 'gene' or 'con', respectively. For instance, in Figure 4 the SHMs of the genes ENSG00000268433 and ENSG00000006047 are organized by condition in a horizontal view. This functionality is particularly useful when comparing gene families. Users can also customize the order of the SHM subplots, by assigning lay.shm='none'. With this setting the SHM subplots are organized according to the gene and condition ordering under ID and data, respectively.

spatial_hm(svg.path=svg.hum, data=se.fil.hum, ID=c('ENSG00000268433', 'ENSG00000006047'), lay.shm='con', width=0.8, height=1, legend.r=1.5, legend.nrow=2, ft.trans=c('g4320'))
## Coordinates: homo_sapiens.brain.svg ... 
## CPU cores: 1 
## Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0001873 UBERON_0001872 UBERON_0002038 UBERON_0001874 UBERON_0001875 UBERON_0002360 
## 
## Duplicated title text detected: hippocampus 
## ggplots/grobs: homo_sapiens.brain.svg ... 
## ggplot: ENSG00000268433, ALS  normal  
## ggplot: ENSG00000006047, ALS  normal  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## ENSG00000268433_ALS_1  ENSG00000268433_normal_1  ENSG00000006047_ALS_1  ENSG00000006047_normal_1
SHMs of two genes. The subplots are organized by "condition" with the `lay.shm='con'` setting.

Figure 4: SHMs of two genes
The subplots are organized by “condition” with the lay.shm='con' setting.

3.2.7 SHM: HTML and Video

SHMs can be saved to interactive HTML files as well as video files. To trigger this export behavior, the argument out.dir needs to be assinged a directory path where the HTML and video files will be stored. Each HTML file contains an interactive SHM with zoom in and out functionality. Hovering over graphics features will display data, gene, condition and other information. The video will play the SHM subplots in the order specified under the lay.shm argument.

The following example saves the interactive HTML and video files under
a directory named tmp.dir.

tmp.dir <- paste0(normalizePath(tempdir(check=TRUE), winslash="/"), '/shm')
spatial_hm(svg.path=svg.hum, data=se.fil.hum, ID=c('ENSG00000268433', 'ENSG00000006047'), lay.shm='con', width=0.8, height=1, legend.r=1.5, legend.nrow=2, out.dir=tmp.dir, ft.trans=c('g4320'))

3.2.8 SHM: Customization

To provide a high level of flexibility, the spatial_hm contains many arguments. An overview of important arguments and their utility is provided in Table 2.


Table 2: List of important argumnets of ‘spatial_hm’.
argument description
svg.path Path of aSVG
data Input data of SummarizedExperiment (SE), data frame, or vector
sam.factor Applies to SE. Column name of sample replicates in colData slot. Default is NULL
con.factor Applies to SE. Column name of condition replicates in colData slot. Default is NULL
ID A character vector of row items for plotting spatial heatmaps
col.com A character vector of color components for building colour scale. Default is c(‘yellow’, ‘orange’,‘red’)
col.bar ‘selected’ or ‘all’, the former means use values of ID to build the colour scale while the latter use all values in data. Default is ‘selected’.
bar.width A numeric of colour bar width. Default is 0.7
trans.scale One of ‘log2’, ‘exp2’, ‘row’, ‘column’, or NULL, which means transform the data by ‘log2’ or ‘2-base expoent’, scale by ‘row’ or ‘column’, or no manipuation respectively.
ft.trans A vector of aSVG features to be transparent. Default is NULL.
legend.r A numeric to adjust the dimension of the legend plot. Default is 1. The larger, the higher ratio of width to height.
sub.title.size The title size of each spatial heatmap subplot. Default is 11.
lay.shm ‘gen’ or ‘con’, applies to multiple genes or conditions respectively. ‘gen’ means spatial heatmaps are organised by genes while ‘con’ organised by conditions. Default is ‘gen’
ncol The total column number of spatial heatmaps, not including legend plot. Default is 2.
ft.legend ‘identical’, ‘all’, or a vector of samples/features in aSVG to show in legend plot. ‘identical’ only shows matching features while ‘all’ shows all features.
legend.ncol, legend.nrow Two numbers of columns and rows of legend keys respectively. Default is NULL, NULL, since they are automatically set.
legend.position the position of legend keys (‘none’, ‘left’, ‘right’,‘bottom’, ‘top’), or two-element numeric vector. Default is ‘bottom’.
legend.key.size, legend.text.size The size of legend keys and labels respectively. Default is 0.5 and 8 respectively.
line.size, line.color The size and colour of all plogyon outlines respectively. Default is 0.2 and ‘grey70’ respectively.
verbose TRUE or FALSE. Default is TRUE and the aSVG features not mapped are printed to R console.
out.dir The directory to save HTML and video files of spatial heatmaps. Default is NULL.

3.3 Mouse Organs

This section generates an SHM plot for mouse data from the Expression Atlas. The code components are very similar to the previous Human Brain example. For brevity, the corresponding text explaining the code has been reduced to a minimum.

3.3.1 Gene Expression Data

The chosen mouse RNA-Seq data compares tissue level gene expression across mammalian species (Merkin et al. 2012). The following searches the Expression Atlas for expression data from ‘heart’ and ‘Mus musculus’.

all.mus <- read_cache(cache.pa, 'all.mus') # Retrieve data from cache.
if (is.null(all.mus)) { # Save downloaded data to cache if it is not cached.
  all.mus <- searchAtlasExperiments(properties="heart", species="Mus musculus")
  save_cache(dir=cache.pa, overwrite=TRUE, all.mus)
}

Among the many matching entries, accession ‘E-MTAB-2801’ will be downloaded.

all.mus[7, ]
## DataFrame with 1 row and 4 columns
##     Accession      Species                  Type                  Title
##   <character>  <character>           <character>            <character>
## 1 E-MTAB-2801 Mus musculus RNA-seq of coding RNA Strand-specific RNA-..
rse.mus <- read_cache(cache.pa, 'rse.mus') # Read data from cache.
if (is.null(rse.mus)) { # Save downloaded data to cache if it is not cached.
  rse.mus <- getAtlasData('E-MTAB-2801')[[1]][[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, rse.mus)
}

The design of the downloaded RNA-Seq experiment is described in the colData slot of rse.mus. The following returns only its first three rows.

colData(rse.mus)[1:3, ]
## DataFrame with 3 rows and 4 columns
##           AtlasAssayGroup     organism organism_part      strain
##               <character>  <character>   <character> <character>
## SRR594393              g7 Mus musculus         brain      DBA/2J
## SRR594394             g21 Mus musculus         colon      DBA/2J
## SRR594395             g13 Mus musculus         heart      DBA/2J

3.3.2 aSVG Image

The following example shows how to download from the above described SVG repositories an aSVG image that matches the tissues and species assayed in the gene expression data set downloaded in the previous subsection. As before the image is saved to a directory named tmp.dir.

tmp.dir <- paste0(normalizePath(tempdir(check=TRUE), winslash="/", mustWork=FALSE), '/shm')
feature.df <- return_feature(feature=c('heart', 'kidney'), species=c('Mus musculus'), keywords.any=TRUE, return.all=FALSE, dir=tmp.dir, remote=TRUE, match.only=FALSE)

To build this vignettes according to the R/Bioconductor package requirements, the following code section uses the aSVG file instance included in the spatialHeatmap package rather than the downloaded instance from the example in the previous step.

feature.df <- return_feature(feature=c('heart', 'kidney'), species=NULL, keywords.any=TRUE, return.all=FALSE, dir=svg.dir, remote=FALSE, match.only=FALSE) 
## Accessing features... 
## arabidopsis.thaliana_organ_shm.svg, arabidopsis.thaliana_organ_shm1.svg, arabidopsis.thaliana_organ_shm2.svg, arabidopsis.thaliana_root.cross_shm.svg, Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## LAYER_OUTLINE 
## 
## arabidopsis.thaliana_root.ebi_shm.svg, Extracted tiny path from path2027 is removed! 
## Extracted tiny path from path2027-3 is removed! 
## arabidopsis.thaliana_root.roottip_shm.svg, Extracted tiny path from path1146-6 is removed! 
## Extracted tiny path from path1146 is removed! 
## arabidopsis.thaliana_shoot.root_shm.svg, Extracted tiny path from path1146 is removed! 
## arabidopsis.thaliana_shoot_shm.svg, Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0014892 
## 
## gallus_gallus.svg, 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0000451 LAYER_EFO 
## 
## homo.sapiens_brain.shiny_shm.svg, Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0001873 UBERON_0001872 UBERON_0002038 UBERON_0001874 UBERON_0001875 UBERON_0002360 
## 
## Duplicated title text detected: hippocampus 
## homo_sapiens.brain.svg, Element "a" is removed: a4174 !
## mus_musculus.male.svg, oryza.sativa_coleoptile.ANT_shm.svg, oryza.sativa_coleoptile.NT_shm.svg, us_map_shm.svg,

Return the names of the matching aSVG files.

unique(feature.df$SVG)
## [1] "gallus_gallus.svg"     "mus_musculus.male.svg"

The following first selects mus_musculus.male.svg as target aSVG, then returns the first three rows of the resulting feature.df, and finally prints the unique set of all aSVG features.

feature.df <- subset(feature.df, SVG=='mus_musculus.male.svg')
feature.df[1:3, ]
##     feature stroke color             id element        parent order
## 10   kidney   0.05  none UBERON_0002113       g     LAYER_EFO     3
## 11    heart   0.05  none UBERON_0000948    path     LAYER_EFO    13
## 12 path4204   0.05  none       path4204       g LAYER_OUTLINE     1
##                      SVG
## 10 mus_musculus.male.svg
## 11 mus_musculus.male.svg
## 12 mus_musculus.male.svg
unique(feature.df[, 1])
##  [1] "kidney"          "heart"           "path4204"        "spleen"         
##  [5] "adrenal.gland"   "colon"           "caecum"          "esophagus"      
##  [9] "tongue"          "testis"          "penis"           "lung"           
## [13] "diaphragm"       "liver"           "brain"           "skeletal.muscle"

Obtain path of target aSVG on user system.

svg.mus <- system.file("extdata/shinyApp/example", "mus_musculus.male.svg", package="spatialHeatmap")

3.3.3 Experimental Design

The following imports a sample target file that is included in this package. To inspect its content, the first three rows of the target file are printed to the screen.

mus.tar <- system.file('extdata/shinyApp/example/target_mouse.txt', package='spatialHeatmap')
target.mus <- read.table(mus.tar, header=TRUE, row.names=1, sep='\t')
target.mus[1:3, ]
##           AtlasAssayGroup     organism organism_part strain
## SRR594393              g7 Mus musculus         brain DBA.2J
## SRR594394             g21 Mus musculus         colon DBA.2J
## SRR594395             g13 Mus musculus         heart DBA.2J
unique(target.mus[, 3])
## [1] "brain"           "colon"           "heart"           "kidney"         
## [5] "liver"           "lung"            "skeletal muscle" "spleen"         
## [9] "testis"

Load custom target data into colData slot.

colData(rse.mus) <- DataFrame(target.mus)

3.3.4 Preprocess Assay Data

The raw RNA-Seq count are preprocessed with the following steps: (1) normalization, (2) aggregation of replicates, and (3) filtering of reliable expression data. The details of these steps are explained in the sub-section above using data from human.

se.nor.mus <- norm_data(data=rse.mus, norm.fun='ESF', log2.trans=TRUE) # Normalization
## Normalising: ESF 
##    type 
## "ratio"
se.aggr.mus <- aggr_rep(data=se.nor.mus, sam.factor='organism_part', con.factor='strain', aggr='mean') # Aggregation of replicates
## Syntactically valid column names are made!
se.fil.mus <- filter_data(data=se.aggr.mus, sam.factor='organism_part', con.factor='strain', pOA=c(0.01, 5), CV=c(0.6, 100), dir=NULL) # Filtering of genes with low counts and variance 
## Syntactically valid column names are made! 
## All values before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   0.000   0.000   2.838   5.282  21.716 
## All coefficient of variances (CVs) before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
## 0.01741 0.29033 1.09806 1.51730 2.34078 5.09902 
## All values after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.0000  0.9781  2.1806  3.4151 21.7158 
## All coefficient of variances (CVs) after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6001  0.8869  1.3158  1.4953  1.9883  5.0990

3.3.5 SHM: Transparency

The pre-processed expression data for gene ‘ENSMUSG00000000263’ is plotted in form of an SHM. In this case the plot includes expression data for 8 tissues across 3 mouse strains.

shm.lis <- spatial_hm(svg.path=svg.mus, data=se.fil.mus, ID=c('ENSMUSG00000000263'), height=0.7, legend.width=0.7, legend.text.size=10, sub.title.size=9, ncol=3, ft.trans=c('skeletal muscle', 'path4204'), legend.nrow=4, line.size=0.2, line.color='grey70')
## Coordinates: mus_musculus.male.svg ... 
## CPU cores: 1 
## Element "a" is removed: a4174 !
## ggplots/grobs: mus_musculus.male.svg ... 
## ggplot: ENSMUSG00000000263, DBA.2J  C57BL.6  CD1  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## ENSMUSG00000000263_DBA.2J_1  ENSMUSG00000000263_C57BL.6_1  ENSMUSG00000000263_CD1_1
SHM of mouse organs. This is a multiple-layer image where the shapes of the 'skeletal muscle' is set transparent to expose 'lung' and 'heart'.

Figure 5: SHM of mouse organs
This is a multiple-layer image where the shapes of the ‘skeletal muscle’ is set transparent to expose ‘lung’ and ‘heart’.

The SHM plots in Figures 5 and below demonstrate the usage of the transparency feature via the ft.trans parameter. Except for the outline layer path4204 interfering with other tissues, the corresponding mouse organ aSVG image includes overlapping tissue layers. In this case the skelectal muscle layer partially overlaps with lung and heart tissues. To view lung and heart in Figure 5, the skelectal muscle tissue and outline are set transparent with ft.trans=c('skeletal muscle', 'path4204'). To view in the same aSVG the skeletal muscle tissue instead, ft.trans is assigned only path4204 as shown below.

To fine control the visual effects in feature rich aSVGs, the line.size and line.color parameters are useful. This way one can adjust the thickness and color of complex structures.

spatial_hm(svg.path=svg.mus, data=se.fil.mus, ID=c('ENSMUSG00000000263'), height=0.6, legend.text.size=10, sub.title.size=9, ncol=3, legend.ncol=2, line.size=0.1, line.color='grey70', ft.trans='path4204')
## Coordinates: mus_musculus.male.svg ... 
## CPU cores: 1 
## Element "a" is removed: a4174 !
## ggplots/grobs: mus_musculus.male.svg ... 
## ggplot: ENSMUSG00000000263, DBA.2J  C57BL.6  CD1  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## ENSMUSG00000000263_DBA.2J_1  ENSMUSG00000000263_C57BL.6_1  ENSMUSG00000000263_CD1_1
SHM of mouse organs. This is a multiple-layer image where the view onto 'lung' and 'heart' is obstructed by displaying the 'skeletal muscle' tissue.

Figure 6: SHM of mouse organs
This is a multiple-layer image where the view onto ‘lung’ and ‘heart’ is obstructed by displaying the ‘skeletal muscle’ tissue.

3.4 Chicken Organs

This section generates an SHM plot for chicken data from the Expression Atlas. The code components are very similar to the Human Brain example. For brevity, the corresponding text explaining the code has been reduced to a minimum.

3.4.1 Gene Expression Data

The chosen chicken RNA-Seq experiment compares the developmental changes across nine time points of seven organs (Cardoso-Moreira et al. 2019).

The following searches the Expression Atlas for expression data from ‘heart’ and ‘gallus’.

all.chk <- read_cache(cache.pa, 'all.chk') # Retrieve data from cache.
if (is.null(all.chk)) { # Save downloaded data to cache if it is not cached.
  all.chk <- searchAtlasExperiments(properties="heart", species="gallus")
  save_cache(dir=cache.pa, overwrite=TRUE, all.chk)
}

Among the matching entries, accession ‘E-MTAB-6769’ will be downloaded.

all.chk[3, ]
## DataFrame with 1 row and 4 columns
##     Accession       Species                  Type                  Title
##   <character>   <character>           <character>            <character>
## 1 E-MTAB-6769 Gallus gallus RNA-seq of coding RNA Chicken RNA-seq time..
rse.chk <- read_cache(cache.pa, 'rse.chk') # Read data from cache.
if (is.null(rse.chk)) { # Save downloaded data to cache if it is not cached.
  rse.chk <- getAtlasData('E-MTAB-6769')[[1]][[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, rse.chk)
}

The design of the downloaded RNA-Seq experiment is described in the colData slot of rse.chk. The following returns only its first three rows.

colData(rse.chk)[1:3, ]
## DataFrame with 3 rows and 8 columns
##            AtlasAssayGroup      organism         strain           genotype
##                <character>   <character>    <character>        <character>
## ERR2576379              g1 Gallus gallus Red Junglefowl wild type genotype
## ERR2576380              g1 Gallus gallus Red Junglefowl wild type genotype
## ERR2576381              g2 Gallus gallus Red Junglefowl wild type genotype
##            developmental_stage         age         sex organism_part
##                    <character> <character> <character>   <character>
## ERR2576379              embryo      10 day      female         brain
## ERR2576380              embryo      10 day      female         brain
## ERR2576381              embryo      10 day      female    cerebellum

3.4.2 aSVG Image

The following example shows how to download from the above introduced SVG repositories an aSVG image that matches the tissues and species assayed in the gene expression data set downloaded in the previous subsection. As before the image is saved to a directory named tmp.dir.

tmp.dir <- paste0(normalizePath(tempdir(check=TRUE), winslash="/", mustWork=FALSE), '/shm')
# Query aSVGs.
feature.df <- return_feature(feature=c('heart', 'kidney'), species=c('gallus'), keywords.any=TRUE, return.all=FALSE, dir=tmp.dir, remote=TRUE, match.only=FALSE)

To build this vignettes according to the R/Bioconductor package requirements, the following code section uses the aSVG file instance included in the spatialHeatmap package rather than the downloaded instance from the previous step.

feature.df <- return_feature(feature=c('heart', 'kidney'), species=c('gallus'), keywords.any=TRUE, return.all=FALSE, dir=svg.dir, remote=FALSE, match.only=FALSE)
## Accessing features... 
## Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0014892 
## 
## gallus_gallus.svg,
feature.df[1:3, ] # A slice of the features.
##           feature stroke   color              id element        parent order
## 1           heart      0    none  UBERON_0000948    path     LAYER_EFO     2
## 2          kidney      0    none  UBERON_0002113    path     LAYER_EFO     3
## 3 chicken_outline      0 #a0a1a2 chicken_outline       g LAYER_OUTLINE     1
##                 SVG
## 1 gallus_gallus.svg
## 2 gallus_gallus.svg
## 3 gallus_gallus.svg

Obtain path of target aSVG on user system.

svg.chk <- system.file("extdata/shinyApp/example", "gallus_gallus.svg", package="spatialHeatmap")

3.4.3 Experimental Design

The following imports a sample target file that is included in this package. To inspect its content, the first three rows of the target file are printed to the screen.

chk.tar <- system.file('extdata/shinyApp/example/target_chicken.txt', package='spatialHeatmap')
target.chk <- read.table(chk.tar, header=TRUE, row.names=1, sep='\t')
target.chk[1:3, ]
##            AtlasAssayGroup      organism         strain           genotype
## ERR2576379              g1 Gallus gallus Red Junglefowl wild type genotype
## ERR2576380              g1 Gallus gallus Red Junglefowl wild type genotype
## ERR2576381              g2 Gallus gallus Red Junglefowl wild type genotype
##            developmental_stage   age    sex organism_part
## ERR2576379              embryo day10 female         brain
## ERR2576380              embryo day10 female         brain
## ERR2576381              embryo day10 female    cerebellum

Load custom target data into colData slot.

colData(rse.chk) <- DataFrame(target.chk)

Return samples used for plotting SHMs.

unique(colData(rse.chk)[, 'organism_part'])
## [1] "brain"      "cerebellum" "heart"      "kidney"     "ovary"     
## [6] "testis"     "liver"

Return conditions considered for plotting downstream SHM.

unique(colData(rse.chk)[, 'age'])
## [1] "day10"  "day12"  "day14"  "day17"  "day0"   "day155" "day35"  "day7"  
## [9] "day70"

3.4.4 Preprocess Assay Data

The raw RNA-Seq count are preprocessed with the following steps: (1) normalization, (2) aggregation of replicates, and (3) filtering of reliable expression data. The details of these steps are explained in the above sub-section on human data.

se.nor.chk <- norm_data(data=rse.chk, norm.fun='ESF', log2.trans=TRUE) # Normalization
## Normalising: ESF 
##    type 
## "ratio"
se.aggr.chk <- aggr_rep(data=se.nor.chk, sam.factor='organism_part', con.factor='age', aggr='mean') # Replicate agggregation using mean 
se.fil.chk <- filter_data(data=se.aggr.chk, sam.factor='organism_part', con.factor='age', pOA=c(0.01, 5), CV=c(0.6, 100), dir=NULL) # Filtering of genes with low counts and varince
## All values before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.6718  5.4389  5.2246  9.0067 23.0323 
## All coefficient of variances (CVs) before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
## 0.01497 0.08457 0.29614 0.79232 1.02089 7.87401 
## All values after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.2118  1.0459  2.0432  2.9370 23.0323 
## All coefficient of variances (CVs) after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6001  0.7793  1.0556  1.3299  1.5950  5.4224

3.4.5 SHM: Time Series

The expression profile for gene ENSGALG00000006346 is plotted across nine time points in four organs in form of a composite SHM with 9 panels. Their layout in three columns is controlled with the argument setting ncol=3. The target organs are labeled by text in legend plot via label=TRUE.

spatial_hm(svg.path=svg.chk, data=se.fil.chk, ID='ENSGALG00000006346', width=0.9, legend.width=0.9, legend.r=1.5, sub.title.size=9, ncol=3, legend.nrow=2, label=TRUE)
## Coordinates: gallus_gallus.svg ... 
## CPU cores: 1 
## Element "a" is removed: a4174 !
## 
## Recommendation: please remove the 'transform' attribute with a 'matrix' value in the following groups by ungrouping and regrouping the respective groups in Inkscape. Otherwise, colors in spatial heatmap might be shifted! 
## UBERON_0014892 
## 
## Features in data not mapped: cerebellum, ovary, testis 
## ggplots/grobs: gallus_gallus.svg ... 
## ggplot: ENSGALG00000006346, day10  day12  day14  day17  day0  day155  day35  day7  day70  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## ENSGALG00000006346_day10_1  ENSGALG00000006346_day12_1  ENSGALG00000006346_day14_1  ENSGALG00000006346_day17_1  ENSGALG00000006346_day0_1  ENSGALG00000006346_day155_1  ENSGALG00000006346_day35_1  ENSGALG00000006346_day7_1  ENSGALG00000006346_day70_1
Time course of chicken organs. The SHM shows the expression profile of a single gene across nine time points and four organs.

Figure 7: Time course of chicken organs
The SHM shows the expression profile of a single gene across nine time points and four organs.

3.5 Arabidopsis Shoot

This section generates an SHM for Arabidopsis thaliana tissues with gene expression data from the Affymetrix microarray technology. The chosen experiment used ribosome-associated mRNAs from several cell populations of shoots and roots that were exposed to hypoxia stress (Mustroph et al. 2009). In this case the expression data will be downloaded from GEO with utilites from the GEOquery package (Davis and Meltzer 2007). The data preprocessing routines are specific to the Affymetrix technology. The remaining code components for generating SHMs are very similar to the previous examples. For brevity, the text in this section explains mainly the steps that are specific to this data set.

3.5.1 Gene Expression Data

The GSE14502 data set will be downloaded with the getGEO function from the GEOquery package. Intermediately, the expression data is stored in an ExpressionSet container (Huber et al. 2015), and then converted to a SummarizedExperiment object.

gset <- read_cache(cache.pa, 'gset') # Retrieve data from cache.
if (is.null(gset)) { # Save downloaded data to cache if it is not cached.
  gset <- getGEO("GSE14502", GSEMatrix=TRUE, getGPL=TRUE)[[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, gset)
}
se.sh <- as(gset, "SummarizedExperiment")

The gene symbol identifiers are extracted from the rowData component to be used as row names. Similarly, one can work with AGI identifiers by providing below AGI under Gene.Symbol.

rownames(se.sh) <- make.names(rowData(se.sh)[, 'Gene.Symbol'])

The following returns a slice of the experimental design stored in the colData slot. Both the samples and conditions are contained in the title column. The samples include promoters (pGL2, pCO2, pSCR, pWOL, p35S), tissues and organs (root atrichoblast epidermis, root cortex meristematic zone, root endodermis, root vasculature, root_total and shoot_total); and the conditions are control and hypoxia.

colData(se.sh)[60:63, 1:4]
## DataFrame with 4 rows and 4 columns
##                            title geo_accession                status
##                      <character>   <character>           <character>
## GSM362227 shoot_hypoxia_pGL2_r..     GSM362227 Public on Oct 12 2009
## GSM362228 shoot_hypoxia_pGL2_r..     GSM362228 Public on Oct 12 2009
## GSM362229 shoot_control_pRBCS_..     GSM362229 Public on Oct 12 2009
## GSM362230 shoot_control_pRBCS_..     GSM362230 Public on Oct 12 2009
##           submission_date
##               <character>
## GSM362227     Jan 21 2009
## GSM362228     Jan 21 2009
## GSM362229     Jan 21 2009
## GSM362230     Jan 21 2009

3.5.2 aSVG Image

In this example, the aSVG image has been generated in Inkscape from the corresponding figure in Mustroph et al. (2009). The resulting custom figure has been included as a sample aSVG file in the spatialHeatmap package. Detailed instructions for generating custom aSVG images in Inkscape are provided in the SVG tutorial.

The annotations in the corresponding aSVG file located under svg.dir can be queried with the return_features function.

feature.df <- return_feature(feature=c('pGL2', 'pRBCS'), species=c('shoot'), keywords.any=TRUE, return.all=FALSE, dir=svg.dir, remote=FALSE, match.only=FALSE)
## Accessing features... 
## Extracted tiny path from path1146-6 is removed! 
## Extracted tiny path from path1146 is removed! 
## arabidopsis.thaliana_shoot.root_shm.svg, Extracted tiny path from path1146 is removed! 
## arabidopsis.thaliana_shoot_shm.svg,

The unique set of the matching aSVG files can be returned as follows.

unique(feature.df$SVG)
## [1] "arabidopsis.thaliana_shoot.root_shm.svg"
## [2] "arabidopsis.thaliana_shoot_shm.svg"

The aSVG file arabidopsis.thaliana_shoot_shm.svg is chosen to generate the SHM in this section.

feature.df <- subset(feature.df, SVG=='arabidopsis.thaliana_shoot_shm.svg')
feature.df[1:3, ]
##        feature    stroke   color          id element    parent order
## 17  shoot_pGL2 0.1500001 #10ddeb  shoot_pGL2       g container     2
## 18 shoot_pRBCS 0.1500001 #7227ab shoot_pRBCS       g container     3
## 19        g258 0.1500001 #f7fcf5        g258       g container     1
##                                   SVG
## 17 arabidopsis.thaliana_shoot_shm.svg
## 18 arabidopsis.thaliana_shoot_shm.svg
## 19 arabidopsis.thaliana_shoot_shm.svg

Obtain full path of target aSVG on user system.

svg.sh <- system.file("extdata/shinyApp/example", "arabidopsis.thaliana_shoot_shm.svg", package="spatialHeatmap")

3.5.3 Experimental Design

The following imports a sample target file that is included in this package. To inspect its content, four selected rows of this target file are printed to the screen.

sh.tar <- system.file('extdata/shinyApp/example/target_arab.txt', package='spatialHeatmap')
target.sh <- read.table(sh.tar, header=TRUE, row.names=1, sep='\t')
target.sh[60:63, ]
##                           col.name      sample condition
## shoot_hypoxia_pGL2_rep1  GSM362227  shoot_pGL2   hypoxia
## shoot_hypoxia_pGL2_rep2  GSM362228  shoot_pGL2   hypoxia
## shoot_control_pRBCS_rep1 GSM362229 shoot_pRBCS   control
## shoot_control_pRBCS_rep2 GSM362230 shoot_pRBCS   control

Return all samples present in target file.

unique(target.sh[, 'sample'])
##  [1] "root_total"      "root_p35S"       "root_pSCR"       "root_pSHR"      
##  [5] "root_pWOL"       "root_pGL2"       "root_pSUC2"      "root_pSultr2.2" 
##  [9] "root_pCO2"       "root_pPEP"       "root_pRPL11C"    "shoot_total"    
## [13] "shoot_p35S"      "shoot_pGL2"      "shoot_pRBCS"     "shoot_pSUC2"    
## [17] "shoot_pSultr2.2" "shoot_pCER5"     "shoot_pKAT1"

Return all conditions present in target file.

unique(target.sh[, 'condition'])
## [1] "control" "hypoxia"

Load custom target data into colData slot.

colData(se.sh) <- DataFrame(target.sh)

3.5.4 Preprocess Assay Data

The downloaded GSE14502 data set has already been normalized with the RMA algorithm (Gautier et al. 2004). Thus, the pre-processing steps can be restricted to the aggregation of replicates and filtering of reliably expressed genes. For the latter, the following code will retain genes with expression values larger than 6 (log2 space) in at least 3% of all samples (pOA=c(0.03, 6)), and with a coefficient of variance (CV) between 0.30 and 100 (CV=c(0.30, 100)).

se.aggr.sh <- aggr_rep(data=se.sh, sam.factor='sample', con.factor='condition', aggr='mean') # Replicate agggregation using mean
se.fil.arab <- filter_data(data=se.aggr.sh, sam.factor='sample', con.factor='condition', pOA=c(0.03, 6), CV=c(0.30, 100), dir=NULL) # Filtering of genes with low intensities and variance
## All values before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   3.345   4.879   6.481   6.763   8.263  15.107 
## All coefficient of variances (CVs) before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
## 0.01047 0.03424 0.05347 0.07706 0.09526 0.54344 
## All values after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   3.644   4.838   6.249   7.364   9.756  15.004 
## All coefficient of variances (CVs) after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.3008  0.3203  0.3385  0.3531  0.3735  0.5434

3.5.5 SHM: Microarray

The expression profile for the HRE2 gene is plotted for the control and the hypoxia treatment across six cell types (Figure 8).

spatial_hm(svg.path=svg.sh, data=se.fil.arab, ID=c("HRE2"), height=0.7, legend.nrow=3, legend.text.size=11)
## Coordinates: arabidopsis.thaliana_shoot_shm.svg ... 
## CPU cores: 1 
## Extracted tiny path from path1146 is removed! 
## Features in data not mapped: root_total, root_p35S, root_pSCR, root_pSHR, root_pWOL, root_pGL2, root_pSUC2, root_pSultr2.2, root_pCO2, root_pPEP, root_pRPL11C, shoot_total, shoot_p35S 
## ggplots/grobs: arabidopsis.thaliana_shoot_shm.svg ... 
## ggplot: HRE2, control  hypoxia  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## HRE2_control_1  HRE2_hypoxia_1
SHM of Arabidopsis shoots. The expression profile of the HRE2 gene is plotted for control and hypoxia treatment across six cell types.

Figure 8: SHM of Arabidopsis shoots
The expression profile of the HRE2 gene is plotted for control and hypoxia treatment across six cell types.

4 Spatiotemporal Heatmaps (STHMs)

The above examples are SHMs plotted at the single spatial dimension. This section showcases the application of SHMs at spatial and temporal dimesions, i.e. data assayed in spatial feature(s) across different development stages.

The data at single spatial dimension contains only two factors: samples and conditions. By contrast, the spatiotemporal data contains three factors: samples, conditions, and times (development stages). There are three alternatives to organize the three factors: 1) combine samples and conditions; 2) combine samples and times; or 3) combine samples, conditions, and times. More details are provided in the Supplementary Section.

Which option to choose depends on the specific data and aSVGs, and the chosen one should achieve optimal visualization. In this example, the third is the best choice and will be showcased in the first part. Meanwhile, for demonstration purpose the second choice will also be illustrated in the second part. In the spatiotemporal application, different development stages can be represented in different aSVG images, and this feature will be presented in the third part.

4.1 Sample-Time-Condition Factor

4.1.1 Gene Expression Data

The data is from the transcriptome analysis on rice coleoptile during germinating and developing stages under anoxia and re-oxygenation (Narsai et al. 2017), which is also downloaded with ExpressionAtlas.

rse.clp <- read_cache(cache.pa, 'rse.clp') # Retrieve data from cache.
if (is.null(rse.clp)) { # Save downloaded data to cache if it is not cached.
  rse.clp <- getAtlasData('E-GEOD-115371')[[1]][[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, rse.clp)
}

4.1.2 Experimental Design

The targets file was prepared according to the experiment design stored in colData slot of res.clp by using the convenient function edit_tar, and pre-packaged in spatialHeatmap.

clp.tar <- system.file('extdata/shinyApp/example/target_coleoptile.txt', package='spatialHeatmap')
target.clp <- read_fr(clp.tar)

The helper function edit_tar is designed to edit entries in the targets file. Below is an example of editing the tissue entries.

cdat <- colData(rse.clp) # Original targets file.
unique(cdat$organism_part) # Original tissues.
## [1] "plant embryo"            "plant embryo coleoptile"
## [3] "coleoptile"
cdat <- edit_tar(cdat, column='organism_part', old=c('plant embryo', 'plant embryo coleoptile'), new=c('embryo', 'embryoColeoptile')) # Replace old entries with desired ones.
unique(cdat$organism_part) # New tissue entries. 
## [1] "embryo"           "embryoColeoptile" "coleoptile"

Inspect the tissues, conditions, and times, where “A” and “N” denote “aerobic” and “anaerobic” respectively.

target.clp[1:3, c(6, 7, 9, 10)] # A slice of the targets file.
##            age organism_part stimulus con
## SRR7265373  0h        embryo  aerobic   A
## SRR7265374  0h        embryo  aerobic   A
## SRR7265375  0h        embryo  aerobic   A
unique(target.clp[, 'age']) # All development stages.
## [1] "0h"     "1h"     "3h"     "12h"    "24h"    "48h"    "72h"    "96h"   
## [9] "72N24A"
unique(target.clp[, 'organism_part']) # All tissues.
## [1] "embryo"           "embryoColeoptile" "coleoptile"
unique(target.clp[, 'stimulus']) # All conditions.
## [1] "aerobic"   "anaerobic" "NA"

Combine sample, time, condition factors using the helper function com_factor. The targets file including the new composite factors (samTimeCon) is loaded to the colData slot in rse.clp internally.

rse.clp <- com_factor(rse.clp, target.clp, factors2com=c('organism_part', 'age', 'con'), sep='.', factor.new='samTimeCon')
## New combined factors: embryo.0h.A embryoColeoptile.1h.A embryoColeoptile.1h.N embryoColeoptile.3h.A embryoColeoptile.3h.N embryoColeoptile.12h.A embryoColeoptile.12h.N embryoColeoptile.24h.A embryoColeoptile.24h.N coleoptile.48h.A coleoptile.48h.N coleoptile.72h.A coleoptile.72h.N coleoptile.96h.A coleoptile.96h.N coleoptile.72N24A.NA
colData(rse.clp)[1:3, c(6, 7, 9:11)]
## DataFrame with 3 rows and 5 columns
##                    age organism_part    stimulus         con  samTimeCon
##            <character>   <character> <character> <character> <character>
## SRR7265373          0h        embryo     aerobic           A embryo.0h.A
## SRR7265374          0h        embryo     aerobic           A embryo.0h.A
## SRR7265375          0h        embryo     aerobic           A embryo.0h.A

Inspect the sample-time-condition composite factors. At least one of the composite factors should have a matching feature counterpart in the aSVG file, otherwise no aSVG file will be returned in the next section.

target.clp <- colData(rse.clp)
unique(target.clp$samTimeCon)
##  [1] "embryo.0h.A"            "embryoColeoptile.1h.A"  "embryoColeoptile.1h.N" 
##  [4] "embryoColeoptile.3h.A"  "embryoColeoptile.3h.N"  "embryoColeoptile.12h.A"
##  [7] "embryoColeoptile.12h.N" "embryoColeoptile.24h.A" "embryoColeoptile.24h.N"
## [10] "coleoptile.48h.A"       "coleoptile.48h.N"       "coleoptile.72h.A"      
## [13] "coleoptile.72h.N"       "coleoptile.96h.A"       "coleoptile.96h.N"      
## [16] "coleoptile.72N24A.NA"

4.1.3 aSVG Image

Similar with the Arabidopsis Shoot example, the aSVG image has been generated in Inkscape from the corresponding figure in Narsai et al. (2017) according to the SVG tutorial, and the resulting custom figure has been included in spatialHeatmap.

Query the aSVG files with one composite factor embryo.0h.A.

feature.df <- return_feature(feature=c('embryo.0h.A', 'embryoColeoptile.1h.A'), species=c('oryza', 'sativa'), keywords.any=FALSE, return.all=FALSE, dir=svg.dir, remote=FALSE, match.only=FALSE)
## Accessing features... 
## oryza.sativa_coleoptile.ANT_shm.svg, oryza.sativa_coleoptile.NT_shm.svg,
feature.df[1:2, ] # The first two rows of the query results.
##                 feature stroke color                    id element    parent
## 1           embryo.0h.A    0.2  none           embryo.0h.A       g container
## 2 embryoColeoptile.1h.A    0.2  none embryoColeoptile.1h.A    path container
##   order                                 SVG
## 1    25 oryza.sativa_coleoptile.ANT_shm.svg
## 2    27 oryza.sativa_coleoptile.ANT_shm.svg

Only one aSVG file oryza.sativa_coleoptile.ANT_shm.svg is retrieved.

unique(feature.df$SVG)
## [1] "oryza.sativa_coleoptile.ANT_shm.svg"

Note no matter how the factors are combined, the composite factors of interest should always have matching counterparts in the aSVG file. In this example, all composite factors are matched to the aSVG.

unique(target.clp$samTimeCon) %in% unique(feature.df$feature)
##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE

Obtain full path of the retrieved aSVG on user system.

svg.clp1 <- system.file("extdata/shinyApp/example", "oryza.sativa_coleoptile.ANT_shm.svg", package="spatialHeatmap")

4.1.4 Preprocess Assay Data

The raw RNA-Seq count are preprocessed with the following steps: (1) normalization, (2) aggregation of replicates, and (3) filtering of reliable expression data. The details of these steps are explained in the above sub-section on human data. The normalization step is same for combined factors sample-time and sample-time-condition, while the aggregation and filtering are different. The difference is reflected by sam.factor and con.factor, and subsequently the column names in resulting assay slot of the SummarizedExperiment object.

se.nor.clp <- norm_data(data=rse.clp, norm.fun='ESF', log2.trans=TRUE) # Normalization
## Normalising: ESF 
##    type 
## "ratio"

Aggregation and filtering by sample-time-condition factor.

se.aggr.clp1 <- aggr_rep(data=se.nor.clp, sam.factor='samTimeCon', con.factor=NULL, aggr='mean') # Replicate agggregation using mean
se.fil.clp1 <- filter_data(data=se.aggr.clp1, sam.factor='samTimeCon', con.factor=NULL, pOA=c(0.07, 7), CV=c(0.7, 100), dir=NULL) # Filtering of genes with low counts and varince.
## All values before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.2995  4.0283  4.3614  7.7436 18.0561 
## All coefficient of variances (CVs) before filtering:
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
## 0.008408 0.087498 0.257247 0.654965 0.847843 4.000000 
## All values after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.4401  2.6058  3.8745  7.1382 15.6921 
## All coefficient of variances (CVs) after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7005  0.7846  0.9030  0.9768  1.0853  1.9504

Since all three factors (conditions, times, tissues) are combined, the resulting data table loses the double underscore string.

assay(se.fil.clp1)[1:3, 1:3] # A slice of the resulting data table.
##              embryo.0h.A embryoColeoptile.1h.A embryoColeoptile.1h.N
## Os01g0106300    2.549855             0.2403387              1.902315
## Os01g0111600   12.116707            12.9343197             12.708776
## Os01g0127600    6.495876             7.3024594              7.443524

4.1.5 STHM: combine sample, time, and condition

The expression profile of gene Os12g0630200 and Os01g0106300 in coleoptile is plotted across eight time points under anoxia and re-oxygenation in form of a composite STHM.

shm.lis <- spatial_hm(svg.path=svg.clp1, data=se.fil.clp1, ID=c('Os12g0630200', 'Os01g0106300'), legend.r=0.7, legend.key.size=0.01, legend.text.size=8, legend.nrow=8, ncol=1, width=0.8, line.size=0)
## Coordinates: oryza.sativa_coleoptile.ANT_shm.svg ... 
## CPU cores: 1 
## ggplots/grobs: oryza.sativa_coleoptile.ANT_shm.svg ... 
## ggplot: Os12g0630200, con  
## ggplot: Os01g0106300, con  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## Os12g0630200_con_1  Os01g0106300_con_1
Spatiotemporal heatmap at sample-time-condition factor. Gene expression profile of two genes in coleoptile across eight time points under anoxia and re-oxygenation is visualized in a composite image.

Figure 9: Spatiotemporal heatmap at sample-time-condition factor
Gene expression profile of two genes in coleoptile across eight time points under anoxia and re-oxygenation is visualized in a composite image.

This STHM example is also deployed as an interacive Shiny app, where STHMs are provided in form of static images, interactive HTML files, and video files. Click here to see this app.

4.2 Sample-Time Factor

This part showcases the usage of sample-time factor. The sample-condition factor could be applied similarly. To obtain optimal result, the data under aerobic is excluded. Since most steps are similar with the sample-time-condition factor, the following process is reduced to minimum.

4.2.1 Gene Expression Data

The same RNA-seq count data from Narsai et al. (2017) is downloaded.

rse.clp <- read_cache(cache.pa, 'rse.clp') # Retrieve data from cache.
if (is.null(rse.clp)) { # Save downloaded data to cache if it is not cached.
  rse.clp <- getAtlasData('E-GEOD-115371')[[1]][[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, rse.clp)
}

4.2.2 Experimental Design

The same targets file with sample-time factor is imported.

clp.tar <- system.file('extdata/shinyApp/example/target_coleoptile.txt', package='spatialHeatmap')
target.clp <- read_fr(clp.tar)

Inspect the samples, conditions, and times.

target.clp[1:3, c(6, 7, 9, 10)] # A slice of the targets file.
##            age organism_part stimulus con
## SRR7265373  0h        embryo  aerobic   A
## SRR7265374  0h        embryo  aerobic   A
## SRR7265375  0h        embryo  aerobic   A
unique(target.clp[, 'age']) # All development stages.
## [1] "0h"     "1h"     "3h"     "12h"    "24h"    "48h"    "72h"    "96h"   
## [9] "72N24A"
unique(target.clp[, 'organism_part']) # All tissues.
## [1] "embryo"           "embryoColeoptile" "coleoptile"
unique(target.clp[, 'stimulus']) # All conditions.
## [1] "aerobic"   "anaerobic" "NA"

Combine sample and time factors, which is the essential difference with sample-time-condition example.

rse.clp <- com_factor(rse.clp, target.clp, factors2com=c('organism_part', 'age'), factor.new='samTime')
## New combined factors: embryo.0h embryoColeoptile.1h embryoColeoptile.3h embryoColeoptile.12h embryoColeoptile.24h coleoptile.48h coleoptile.72h coleoptile.96h coleoptile.72N24A
target.clp <- colData(rse.clp)
target.clp[1:3, ]
## DataFrame with 3 rows and 11 columns
##            AtlasAssayGroup           genotype     organism    cultivar
##                <character>        <character>  <character> <character>
## SRR7265373              g1 wild type genotype Oryza sativa      Amaroo
## SRR7265374              g1 wild type genotype Oryza sativa      Amaroo
## SRR7265375              g1 wild type genotype Oryza sativa      Amaroo
##            developmental_stage         age organism_part environmental_history
##                    <character> <character>   <character>           <character>
## SRR7265373                seed          0h        embryo            etiolation
## SRR7265374                seed          0h        embryo            etiolation
## SRR7265375                seed          0h        embryo            etiolation
##               stimulus         con     samTime
##            <character> <character> <character>
## SRR7265373     aerobic           A   embryo.0h
## SRR7265374     aerobic           A   embryo.0h
## SRR7265375     aerobic           A   embryo.0h

4.2.3 aSVG Image

Similarly the custom aSVG image was generated in Inkscape from the corresponding figure in Narsai et al. (2017) according to the SVG tutorial and included in spatialHeatmap.

Query the aSVG files.

feature.df <- return_feature(feature=c('embryo.0h', 'embryoColeoptile1h'), species=c('oryza', 'sativa'), keywords.any=FALSE, return.all=FALSE, dir=svg.dir, remote=FALSE, match.only=FALSE)
## Accessing features... 
## oryza.sativa_coleoptile.ANT_shm.svg, oryza.sativa_coleoptile.NT_shm.svg,
feature.df[1:2, ] # The first two rows of the query results.
##        feature stroke   color           id element    parent order
## 1    embryo.0h    0.2    none    embryo.0h       g container    25
## 2 rect1033_LGD    0.2 #3f1d38 rect1033_LGD    path container     1
##                                  SVG
## 1 oryza.sativa_coleoptile.NT_shm.svg
## 2 oryza.sativa_coleoptile.NT_shm.svg

Only one aSVG file oryza.sativa_coleoptile.NT_shm.svg is retrieved.

unique(feature.df$SVG)
## [1] "oryza.sativa_coleoptile.NT_shm.svg"

Note no matter how the factors are combined, the composite factor of interest should always have matching counterparts in the aSVG file.

unique(target.clp$samTime) %in% unique(feature.df$feature)
## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

Obtain full path of the retrieved aSVG on user system.

svg.clp2 <- system.file("extdata/shinyApp/example", "oryza.sativa_coleoptile.NT_shm.svg", package="spatialHeatmap")

4.2.4 Preprocess Assay Data

The raw RNA-Seq count are preprocessed with the following steps: (1) normalization, (2) aggregation of replicates, and (3) filtering of reliable expression data. The normalization step is the same for composite factors sample-time and sample-time-condition, while the aggregation and filtering are different. The difference is reflected by sam.factor and con.factor, and subsequently the column names in the assay slot of the resulting SummarizedExperiment object.

se.nor.clp <- norm_data(data=rse.clp, norm.fun='ESF', log2.trans=TRUE) # Normalization
## Normalising: ESF 
##    type 
## "ratio"

Aggregation and filtering by sample-time factor.

se.aggr.clp2 <- aggr_rep(data=se.nor.clp, sam.factor='samTime', con.factor='stimulus', aggr='mean') # Replicate agggregation using mean. 
se.fil.clp2 <- filter_data(data=se.aggr.clp2, sam.factor='samTime', con.factor='stimulus', pOA=c(0.07, 7), CV=c(0.7, 100), dir=NULL) # Filtering of genes with low counts and varince.
## All values before filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.2995  4.0283  4.3614  7.7436 18.0561 
## All coefficient of variances (CVs) before filtering:
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
## 0.008408 0.087498 0.257247 0.654965 0.847843 4.000000 
## All values after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.0000  0.4401  2.6058  3.8745  7.1382 15.6921 
## All coefficient of variances (CVs) after filtering:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.7005  0.7846  0.9030  0.9768  1.0853  1.9504

Since only sample and time factors are combined, the resulting data table preserves the double underscore string, which is different from the sample-time-condition example.

df.fil.clp <- assay(se.fil.clp2) 
df.fil.clp[1:3, 1:3] # A slice of the resulting data table.
##              embryo.0h__aerobic embryoColeoptile.1h__aerobic
## Os01g0106300           2.549855                    0.2403387
## Os01g0111600          12.116707                   12.9343197
## Os01g0127600           6.495876                    7.3024594
##              embryoColeoptile.1h__anaerobic
## Os01g0106300                       1.902315
## Os01g0111600                      12.708776
## Os01g0127600                       7.443524

The optimal viusalization on complete data is achieved on sample-time-condition factor. To also obtain the best result on sample-time factor, the data under aerobic is excluded.

df.fil.clp1 <- df.fil.clp[, !grepl('__aerobic', colnames(df.fil.clp))] # Exclude aerobic data.  
df.fil.clp1[1:3, 1:3] # A slice of the data table without aerobic data.
##              embryoColeoptile.1h__anaerobic embryoColeoptile.3h__anaerobic
## Os01g0106300                       1.902315                       1.357282
## Os01g0111600                      12.708776                      12.531359
## Os01g0127600                       7.443524                       6.919786
##              embryoColeoptile.12h__anaerobic
## Os01g0106300                       2.9825250
## Os01g0111600                       9.7997716
## Os01g0127600                       0.9402776

4.2.5 STHM: combine sample and time

The expression profile of gene Os12g0630200 in coleoptile is plotted across eight time points under anoxia and re-oxygenation respectively.

shm.lis <- spatial_hm(svg.path=svg.clp2, data=df.fil.clp1, ID=c('Os12g0630200'), legend.r=0.9, legend.key.size=0.02, legend.text.size=9, legend.nrow=8, ncol=1, line.size=0)
## Coordinates: oryza.sativa_coleoptile.NT_shm.svg ... 
## CPU cores: 1 
## ggplots/grobs: oryza.sativa_coleoptile.NT_shm.svg ... 
## ggplot: Os12g0630200, anaerobic  NA  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## Os12g0630200_anaerobic_1  Os12g0630200_NA_1
Spatiotemporal heatmap at sample-time factor. Gene expression profile of one gene in coleoptile across eight time points under anoxia and re-oxygenation is visualized in two images.

Figure 10: Spatiotemporal heatmap at sample-time factor
Gene expression profile of one gene in coleoptile across eight time points under anoxia and re-oxygenation is visualized in two images.

4.3 Multiple aSVGs

In the spatiotemporal application, different development stages may need to be represented in separate aSVG images. In that case, the spatial_hm function is able to arrange multiple aSVGs in a single SHM plot. To organize the subplots, the names of the separate aSVG files are expected to include the following suffixes: *_shm1.svg, *_shm2.svg, etc. The paths to the aSVG files are provided under the svg.path argument. By default, every aSVG image will have a legend plot on the right. The legend argument provides fine control over which legend plots to display.

As a simple toy example, the following stores random numbers in a data.frame.

df.random <- data.frame(matrix(sample(x=1:100, size=50, replace=TRUE), nrow=10))
colnames(df.random) <- c('shoot_totalA__condition1', 'shoot_totalA__condition2', 'shoot_totalB__condition1', 'shoot_totalB__condition2', 'notMapped') # Assign column names
rownames(df.random) <- paste0('gene', 1:10) # Assign row names 
df.random[1:3, ]
##       shoot_totalA__condition1 shoot_totalA__condition2
## gene1                       66                       17
## gene2                       95                       40
## gene3                       74                        9
##       shoot_totalB__condition1 shoot_totalB__condition2 notMapped
## gene1                       17                       91         5
## gene2                       90                       69        64
## gene3                       88                       72        37

Next the paths to the aSVG files are obtained, here for younger and older plants using *_shm1 and *_shm1, respectively, which are made from Mustroph et al. (2009).

svg.sh1 <- system.file("extdata/shinyApp/example", "arabidopsis.thaliana_organ_shm1.svg", package="spatialHeatmap")
svg.sh2 <- system.file("extdata/shinyApp/example", "arabidopsis.thaliana_organ_shm2.svg", package="spatialHeatmap")

The following generates the corresponding SHMs plot for gene1. The orginal image dimensions can be preserved by assigning TRUE to the preserve.scale argument.

spatial_hm(svg.path=c(svg.sh1, svg.sh2), data=df.random, ID=c('gene1'), width=0.7, legend.r=0.9, legend.width=1, preserve.scale=TRUE) 
## Coordinates: arabidopsis.thaliana_organ_shm1.svg ... 
## CPU cores: 1 
## Coordinates: arabidopsis.thaliana_organ_shm2.svg ... 
## CPU cores: 1 
## Features in data not mapped: shoot_totalB, notMapped 
## Features in data not mapped: shoot_totalA, notMapped 
## ggplots/grobs: arabidopsis.thaliana_organ_shm1.svg ... 
## ggplot: gene1, condition1  condition2  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## gene1_condition1_1  gene1_condition2_1  
## ggplots/grobs: arabidopsis.thaliana_organ_shm2.svg ... 
## ggplot: gene1, condition1  condition2  
## Legend plot ... 
## CPU cores: 1 
## Converting "ggplot" to "grob" ... 
## gene1_condition1_2  gene1_condition2_2
Spatial heatmap of Arabidopsis at two growth stages. The expression profile of gene1 under condition1 and condition2 is plotted for two growth stages (top and bottom row).

Figure 11: Spatial heatmap of Arabidopsis at two growth stages
The expression profile of gene1 under condition1 and condition2 is plotted for two growth stages (top and bottom row).

Note in Figure 11 shoots have thicker outlines than roots. This is another function of spatial_hm, i.e. preserves the outline thicknesses defined in aSVG files. This feature is particularly useful in cellular SHMs where different cell types have different cell-wall thicknesses. The outline widths can be updated with update_feature programatically or with Inkscape manually. The former is illustrated in the Supplementary Section.

5 Multi-Factor Spatial Heatmaps

In principle, the spatialHeatmap is extendable to as many factors (e.g. samples, conditions, times) as possible. The most common scenario involves only two factors of samples and conditions (Section 3). If more factors are relevant such as development stages, geographical locations, genotypes, etc, all or selected factors should be combined to generate composite factors. The spatiotemporal section is an illustration of three factors. Similar combining strategies should be appied in cases of four or more factors. A rule of thumb is the composite factors of interest must have a matching counterpart in the aSVG file, otherwise target spatial features are not painted in spatial heatmaps.

6 Matrix Heatmaps

SHMs are suitable for comparing assay profiles among small number of items (e.g. few genes or proteins) across cell types and conditions. To also support analysis routines of larger number of items, spatialHeatmap integrates functionalities for identifying groups of items with similar and/or dissimilar assay profiles, and subsequently analyzing the results with data mining methods methods that scale to larger numbers of items than SHMs, such as hierarchical clustering and network analysis methods. The following introduces both approaches using as sample data the gene expression data from Arabidopsis shoots from the previous section.

To identify similar items, the submatrix function can be used. The latter identifies items sharing similar profiles with one or more query items of interest. The given example uses correlation coefficients as similarity metric. Three filtering parameters are provided to control the similarity and number of items in the result. First, the p argument allows to restrict the number of similar items to return based on a percentage cutoff relative to the number of items in the assay data set (e.g. 1% of the top most similar items). Second, a fixed number n of the most similar items can be returned. Third, all items above a user definable correlation coefficient cutoff value can be returned, such as a Pearson correlation coefficient (PCC) of at least 0.6. If several query items are provided then the function returns the similar genes for each query, while assuring uniqueness among items in the result.

The following example uses as query the two genes: ‘RCA’ and ‘HRE2’. The ann argument corresponds to the column name in the rowData slot containing gene annotation information. The latter is only relevant if users want to see these annotations when mousing over a node in the interactive network plot generated in the next section.

sub.mat <- submatrix(data=se.fil.arab, ann='Target.Description', ID=c('RCA', 'HRE2'), p=0.1)

The result from the previous step is the assay matrix subsetted to the genes sharing similar assay profiles with the query genes ‘RCA’ and ‘HRE2’.

sub.mat[c('RCA', 'HRE2'), c(1:3, 37)] # Subsetted assay matrix
##      root_total__control root_total__hypoxia root_p35S__control
## RCA             6.569305            6.416811           7.443822
## HRE2            5.486920           11.370161           5.578123
##                                                    Target.Description
## RCA  hypothetical protein ;supported by full-length cDNA: Ceres:7114.
## HRE2                         putative AP2 domain transcription factor

Subsequently, hierarchical clustering is applied to the subsetted assay matrix containing only the genes that share profile similarities with the query genes ‘RCA’ and ‘HRE2’. The clustering result is displayed as a matrix heatmap where the rows and columns are sorted by the corresponding hierarchical clustering dendrograms (Figure 12). The position of the query genes (‘RCA’ and ‘HRE2’) is indicated in the heatmap by black lines. Setting static=FALSE will launch the interactive mode, where users can zoom into the heatmap by selecting subsections in the image or zoom out by double clicking.

matrix_hm(ID=c('RCA', 'HRE2'), data=sub.mat, angleCol=80, angleRow=35, cexRow=0.8, cexCol=0.8, margin=c(10, 6), static=TRUE, arg.lis1=list(offsetRow=0.01, offsetCol=0.01))
Matrix Heatmap. Rows are genes and columns are samples. The input genes are tagged by black lines.

Figure 12: Matrix Heatmap
Rows are genes and columns are samples. The input genes are tagged by black lines.

7 Network Graphs

7.1 Module Identification

Network analysis is performed with the WGCNA algorithm (Langfelder and Horvath 2008; Ravasz et al. 2002) using as input the subsetted assay matrix generated in the previous section. The objective is to identify network modules that can be visualized in the following step in form of network graphs. Applied to the gene expression sample data used here, these network modules represent groups of genes sharing highly similar expression profiles. Internally, the network module identification includes five major steps. First, a correlation matrix is computed using distance or correlation-based similarity metrics. Second, the obtained matrix is transformed into an adjacency matrix defining the connections among items. Third, the adjacency matrix is used to calculate a topological overlap matrix (TOM) where shared neighborhood information among items is used to preserve robust connections, while removing spurious connections. Fourth, the distance transformed TOM is used for hierarchical clustering. To maximize time performance, the hierarchical clustering is performed with the flashClust package (Langfelder and Horvath 2012). Fifth, network modules are identified with the dynamicTreeCut package (Langfelder, Zhang, and Steve Horvath 2016). Its ds (deepSplit) argument can be assigned integer values from 0 to 3, where higher values increase the stringency of the module identification process. To simplify the network module idenification process with WGCNA, the individual steps can be executed with a single function called adj_mod. The result is a list containing the adjacency matrix and the final module assignments stored in a data.frame. Since the interactive network feature used in the visualization step below performs best on smaller modules, only modules are returned that were obtained with stringent ds settings (here ds=2 and ds=3).

adj.mod <- adj_mod(data=sub.mat)

A slice of the adjacency matrix is shown below.

adj.mod[['adj']][1:3, 1:3]
##                 CA1    PSAH.1 AT2G26500
## CA1       1.0000000 0.9514016 0.9636366
## PSAH.1    0.9514016 1.0000000 0.9611725
## AT2G26500 0.9636366 0.9611725 1.0000000

The module assignments are stored in a data frame. Its columns contain the results for the ds=2 and ds=3 settings. Integer values \(>0\) are the module labels, while \(0\) indicates unassigned items. The following returns the first three rows of the module assignment result.

adj.mod[['mod']][1:3, ] 
##           2 3
## CA1       1 1
## PSAH.1    1 1
## AT2G26500 1 1

7.2 Module Visualization

Network modules can be visualized with the network function. To plot a module containing an item (gene) of interest, its ID (e.g. ‘HRE2’) needs to be provided under the corresponding argument. Typically, this could be one of the items chosen for the above SHM plots. There are two modes to visualize the selected module: static or interactive. Figure 13 was generated with static=TRUE. Setting static=FALSE will generate the interactive version. In the network plot shown below the nodes and edges represent genes and their interactions, respectively. The thickness of the edges denotes the adjacency levels, while the size of the nodes indicates the degree of connectivity of each item in the network. The adjacency and connectivity levels are also indicated by colors. For example, in Figure 13 connectivity increases from “turquoise” to “violet”, while the adjacency increases from “yellow” to “blue”. If a gene of interest has been assigned under ID, then its ID is labeled in the plot with the suffix tag: ’*_target’.

network(ID="HRE2", data=sub.mat, adj.mod=adj.mod, adj.min=0.90, vertex.label.cex=1.2, vertex.cex=2, static=TRUE)
Static network. Node size denotes gene connectivity while edge thickness stands for co-expression similarity.

Figure 13: Static network
Node size denotes gene connectivity while edge thickness stands for co-expression similarity.

Setting static=FALSE launches the interactive network. In this mode there is an interactive color bar that denotes the gene connectivity. To modify it, the color lables need to be provided in a comma separated format, e.g.: yellow, orange, red. The latter would indicate that the gene connectivity increases from yellow to red.

If the subsetted expression matrix contains gene/protein annotation information in the last column, then it will be shown when moving the cursor over a network node.

network(ID="HRE2", data=sub.mat,  adj.mod=adj.mod, static=FALSE)

8 Shiny App

In additon to running spatialHeatmap from R, the package includes a Shiny App that provides access to the same functionalities from an intuitive-to-use web browser interface. Apart from being very user-friendly, this App conveniently organizes the results of the entire visualization workflow in a single browser window with options to adjust the parameters of the individual components interactively. For instance, genes can be selected and replotted in the SHM simply by clicking the corresponding rows in the expression table included in the same window. This representation is very efficient in guiding the interpretation of the results in a visual and user-friendly manner. For testing purposes, the spatialHeatmap Shiny App also includes ready-to-use sample expression data and aSVG images along with embedded user instructions.

8.1 Local System

The Shiny App of spatialHeatmap can be launched from an R session with the following function call.

shiny_shm()

The dashboard panels of the Shiny App are organized as follows:

  1. Upload: menu for uploading custom files, selecting default files, or downloading example files.
  2. Data Matrix: scrollable assay matrix uploaded by users
  3. Spatial Heatmap: spatially colored images based on aSVG images selected and/or uploaded by user
  4. Matrix Heatmap: hierarchical clustering results of user selected items along with nearest neighbors showing most similar abundance profiles
  5. Network Graph: interactive network graph for selected module
  6. Parameter Control Menus: postioned on top of each visualization panel

A screenshot is shown below depicting an SHM plot generated with the Shiny App of spatialHeatmap (Figure 14).

Screenshot of spatialHeatmap's Shiny App.

Figure 14: Screenshot of spatialHeatmap’s Shiny App

After launching, the Shiny App displays by default one of the included data sets.

The assay data and aSVG images are uploaded to the Shiny App as tabular files (e.g. in CSV or TSV format) and SVG files, respectively. To also allow users to upload gene expression data stored in SummarizedExperiment objects, one can export it from R to a tabular file with the filter_data function, where the user specifies the directory path under the dir argument. This will create in the target directory a tablular file named customData.txt in TSV format. The column names in this file preserve the experimental design information from the colData slot by concatenating the corresponding sample and condition information separated by double underscores. An example of this format is shown in Table 1.

se.fil.arab <- filter_data(data=se.aggr.sh, ann="Target.Description", sam.factor='sample', con.factor='condition', pOA=c(0.03, 6), CV=c(0.30, 100), dir='./')

To interactively access gene-, transcript- or protein-level annotations in the plots and tables of the Shiny App, such as viewing functional descriptions by moving the cursor over network nodes, the corresponding annotation column needs to be present in the rowData slot and its column name assigned to the ann argument. In the exported tabular file, the extra annotation column is appended to the expression matrix.

8.2 Server Deployment

As most Shiny Apps, spatialHeatmap can be deployed as a centralized web service. A major advantage of a web server deployment is that the functionalities can be accessed remotely by anyone on the internet without the need to use R on the user system. For deployment one can use custom web servers or cloud services, such as AWS, GCP or shinysapps.io. An example web instance for testing spatialHeatmap online is available here.

8.3 Custom Shiny App

The spatialHeatmap package also allows users to create customized Shiny App instances using the custom_shiny function. This function provides options to include custom example data and aSVGs, and define default values within most visualization panels (e.g. color schemes, image dimensions). For details users want to consult the help file of the custom_shiny function. To maximize flexibilty, the default parameters are stored in a yaml file on the Shiny App. This makes it easy to refine and optimize default parameters simply by changing this yaml file.

8.4 Database Backend

To maintain scalability, the customized Shiny app is designed to work with HDF5-based database (Fischer, Smith, and Pau 2020; Pagès 2020), which enables users to incorporate data and aSVGs in a batch. The database is constructed with the function write_hdf5. Basically, the accepted data formats are data.frame or SummarizedExperiment. Each data set is saved in an independent HDF5 database. Meanwhile, a pairing table describing matchings between data and aSVGs is required. All individual databases and the pairing table are then compressed in the file “data_shm.tar”. Accordingly, all aSVG files should be compressed in another tar file such as “aSVGs.tar”. Finally, these two tar files are included in the Shiny app by feeding their paths in a list to custom_shiny.

Except for user-provided data, the database is able to store data sets downloaded from GEO and Expression Atlas. The detailed examples of the database utility are documented in the help file of write_hdf5.

9 Supplementary Section

9.1 Numeric Data

The numceric data used to color the features in aSVG images can be provided as three different object types including vector, data.frame and SummerizedExperiment. When working with complex omics-based assay data then the latter provides the most flexibility, and thus should be the preferred container class for managing numeric data in spatialHeatmap. Both data.frame and SummarizedExperiment can hold data from many measured items, such as many genes or proteins. In contrast to this, the vector class is only suitable for data from single items. Due to its simplicity this less complex container is often useful for testing or when dealing with simple data sets.

In data assayed only at spatial dimension, there are two factors samples and conditions, while data assayed at spatial and temporal dimension contains an additional factor time points or development stages. The spatialHeatmap is able to work with both data types. In this section, the application of SHMs on spatial data is explained first in terms of the three object types, which is more popular. Later, the spatiotemporal usage of SHMs is presented in a specific subsection.

9.1.1 Object Types

This subsection refers to data assayed only at spatial dimension, where two factors samples and conditions are involved.

9.1.1.1 vector

When using numeric vectors as input to spatial_hm, then their name slot needs to be populated with strings matching the feature names in the corresponding aSVG. To also specify conditions, their labels need to be appended to the feature names with double underscores as separator, i.e. ’feature__condition’.

The following example replots the toy example for two spatial features (‘occipital lobe’ and ‘parietal lobe’) and two conditions (‘1’ and ‘2’).

vec <- sample(x=1:100, size=5) # Random numeric values
names(vec) <- c('occipital lobe__condition1', 'occipital lobe__condition2', 'parietal lobe__condition1', 'parietal lobe__condition2', 'notMapped') # Assign unique names to random values
vec
## occipital lobe__condition1 occipital lobe__condition2 
##                         13                          7 
##  parietal lobe__condition1  parietal lobe__condition2 
##                         43                         37 
##                  notMapped 
##                         51

With this configuration the resulting plot contains two spatial heatmap plots for the human brain, one for ‘condition 1’ and another one for ‘contition 2’. To keep the build time and storage size of this package to a minimum, the spatial_hm function call in the code block below is not evaluated. Thus, the corresponding SHM is not shown in this vignette.

spatial_hm(svg.path=svg.hum, data=vec, ID='toy', ncol=1, legend.r=1.2, sub.title.size=14, ft.trans='g4320')

9.1.1.2 data.frame

Compared to the above vector input, data.frames are structured here like row-wise appended vectors, where the name slot information in the vectors is stored in the column names. Each row also contains a name that corresponds to the corresponding item name, such as a gene ID. The naming of spatial features and conditions in the column names follows the same conventions as the naming used for the name slots in the above vector example.

The following illustrates this with an example where a numeric data.frame with random numbers is generated containing 20 rows and 5 columns. To avoid name clashes, the values in the rows and columns should be unique.

df.test <- data.frame(matrix(sample(x=1:1000, size=100), nrow=20)) # Create numeric data.frame
colnames(df.test) <- names(vec) # Assign column names
rownames(df.test) <- paste0('gene', 1:20) # Assign row names
df.test[1:3, ]
##       occipital lobe__condition1 occipital lobe__condition2
## gene1                        142                        934
## gene2                        798                        147
## gene3                          5                        386
##       parietal lobe__condition1 parietal lobe__condition2 notMapped
## gene1                       987                       968       751
## gene2                       646                       444        32
## gene3                       790                       756       407

With the resulting data.frame one can generate the same SHM as in the previous example, that used a named vector as input to the spatial_hm function. Additionally, one can now select each row by its name (here gene ID) under the ID argument.

spatial_hm(svg.path=svg.hum, data=df.test, ID=c('gene1'), ncol=1, legend.r=1.2, sub.title.size=14)

Additional information can be appended to the data.frame column-wise, such as annotation data including gene descriptions. This information can then be displayed interactively in the network plots of the Shiny App by placing the curser over network nodes.

df.test$ann <- paste0('ann', 1:20)
df.test[1:3, ]
##       occipital lobe__condition1 occipital lobe__condition2
## gene1                        142                        934
## gene2                        798                        147
## gene3                          5                        386
##       parietal lobe__condition1 parietal lobe__condition2 notMapped  ann
## gene1                       987                       968       751 ann1
## gene2                       646                       444        32 ann2
## gene3                       790                       756       407 ann3

9.1.1.3 SummarizedExperiment

The SummarizedExperiment class is a much more extensible and flexible container for providing metadata for both rows and columns of numeric data stored in tabular format.

To import experimental design information from tabular files, users can provide a target file that will be stored in the colData slot of the SummarizedExperiment (SE, Morgan et al. (2018)) object. In other words, the target file provides the metadata for the columns of the numeric assay data. Usually, the target file contains at least two columns: one for the features/samples and one for the conditions. Replicates are indicated by identical entries in these columns. The actual numeric matrix representing the assay data is stored in the assay slot, where the rows correspond to items, such as gene IDs. Optionally, additional annotation information for the rows (e.g. gene descriptions) can be stored in the rowData slot.

For constructing a valid SummarizedExperiment object, that can be used by the spatial_hm function, the target file should meet the following requirements.

  1. It should be imported with read.table or read.delim into a data.frame or the data.frame can be constructed in R on the fly (as shown below).

  2. It should contain at least two columns. One column represents the features/samples and the other one the conditions. The rows in the target file correspond to the columns of the numeric data stored in the assay slot. If the condition column is empty, then the same condition is assumed under the corresponding features/samples entry.

  3. The feature/sample names must have matching entries in corresponding aSVG to be considered in the final SHM. Note, the double underscore is a special string that is reserved for specific purposes in spatialHeatmap, and thus should be avoided for naming feature/samples and conditions.

The following example illustrates the design of a valid SummarizedExperiment object for generating SHMs. In this example, the ‘occipital lobe’ tissue has 2 conditions and each condition has 2 replicates. Thus, there are 4 assays for occipital lobe, and the same design applies to the parietal lobe tissue.

sample <- c(rep('occipital lobe', 4), rep('parietal lobe', 4))
condition <- rep(c('condition1', 'condition1', 'condition2', 'condition2'), 2)
target.test <- data.frame(sample=sample, condition=condition, row.names=paste0('assay', 1:8))
target.test
##                sample  condition
## assay1 occipital lobe condition1
## assay2 occipital lobe condition1
## assay3 occipital lobe condition2
## assay4 occipital lobe condition2
## assay5  parietal lobe condition1
## assay6  parietal lobe condition1
## assay7  parietal lobe condition2
## assay8  parietal lobe condition2

The assay slot is populated with a 8 x 20 data.frame containing random numbers. Each column corresponds to an assay in the target file (here imported into colData), while each row corresponds to a gene.

df.se <- data.frame(matrix(sample(x=1:1000, size=160), nrow=20))
rownames(df.se) <- paste0('gene', 1:20)
colnames(df.se) <- row.names(target.test)
df.se[1:3, ]
##       assay1 assay2 assay3 assay4 assay5 assay6 assay7 assay8
## gene1    723    427    313    167     92    131    617     80
## gene2     13    739    712    324    700    227    534    682
## gene3    221    223    809    906    961    572    772    721

Next, the final SummarizedExperiment object is constructed by providing the numeric and target data under the assays and colData arguments, respectively.

se <- SummarizedExperiment(assays=df.se, colData=target.test)
se
## class: SummarizedExperiment 
## dim: 20 8 
## metadata(0):
## assays(1): ''
## rownames(20): gene1 gene2 ... gene19 gene20
## rowData names(0):
## colnames(8): assay1 assay2 ... assay7 assay8
## colData names(2): sample condition

If needed row-wise annotation information (e.g. for genes) can be included in the SummarizedExperiment object as well. This can be done during the construction of the initial object, or as below by injecting the information into an existing SummarizedExperiment object.

rowData(se) <- df.test['ann']

In this simple example, possible normalization and filtering steps are skipped. Yet, the aggregation of replicates is performed as shown below.

se.aggr <- aggr_rep(data=se, sam.factor='sample', con.factor='condition', aggr='mean')
## Syntactically valid column names are made!
assay(se.aggr)[1:3, ]
##       occipital.lobe__condition1 occipital.lobe__condition2
## gene1                        575                      240.0
## gene2                        376                      518.0
## gene3                        222                      857.5
##       parietal.lobe__condition1 parietal.lobe__condition2
## gene1                     111.5                     348.5
## gene2                     463.5                     608.0
## gene3                     766.5                     746.5

With the fully configured SummarizedExperiment object, a similar SHM is plotted as in the previous examples.

spatial_hm(svg.path=svg.hum, data=se.aggr, ID=c('gene1'), ncol=1, legend.r=1.2, sub.title.size=14, ft.trans=c('g4320'))

9.1.2 Spatiotemporal Data

The above explanations on the three object types are applicable to data at a single spatial dimension directly. If the data is measured at spatial and temporal dimension, there are three factors: samples, conditions, and time points such as development stages. The three object types are still applicable, but the formatting convention is slightly different.

Specifically, there are three options to format the spatiotemporal data: 1) Combine samples and conditions. In vector names and data.frame column names, the composite sample-condition factor and time factor should be concatenated by double underscore, while in SummarizedExperiment the former and latter should be regarded as the “sample” and “condition” columns respectively; 2) Combine samples and times. In vector names and data.frame column names, the composite sample-time factor and condition factor should be concatenated by double underscore (see here), while in SummarizedExperiment the former and latter should be regarded as the “sample” and “condition” columns respectively; or 3) Combine samples, conditions, and times. The composite sample-time-condition factor will be the full names in vector and full column names in data.frame without the double underscore (see here), while in SummarizedExperiment they will be the “sample” column and the “condition” column will be ignored (see here).

Which option to choose depends on the specific data and aSVGs, and the chosen option is expected to achieve optimal visualization. Regardless of the options, the pivotal requirement that target spatial features in aSVG must have matching counterparts in data should always be fulfilled (see here).

9.2 aSVG File

9.2.1 aSVG repository

A public aSVG repository, that can be used by spatialHeatmap directly, is the one maintained by the EBI Gene Expression Group. It contains annatomical aSVG images from different species. The same aSVG images are also used by the web service of the Expression Atlas project. In addition, the spatialHeatmap has its own repository called spatialHeatmap aSVG Repository, that stores custom aSVG files developed for this project (e.g. Figure 8).

If users cannot find a suitable aSVG image in these two repositories, we have developed a step-by-step SVG tutorial for creating custom aSVG images. For example, the BAR eFP browser at University of Toronto contains many anatomical images. These images can be used as templates in the SVG tutorial to construct custom aSVGs.

Moreover, in the future we will add more aSVGs to our repository, and users are welcome to deposit their own aSVGs to this repository to share them with the community.

9.2.2 Update aSVG features

To create and edit existing feature identifiers in aSVGs, the update_feature function can be used. The demonstration below, creates an empty folder tmp.dir1 and copies into it the homo_sapiens.brain.svg image provided by the spatialHeatmap package. Subsequently, selected feature annotations are updated in this file.

tmp.dir1 <- paste0(normalizePath(tempdir(check=TRUE), winslash="/", mustWork=FALSE), '/shm1')
if (!dir.exists(tmp.dir1)) dir.create(tmp.dir1)
svg.hum <- system.file("extdata/shinyApp/example", 'homo_sapiens.brain.svg', package="spatialHeatmap") 
file.copy(from=svg.hum, to=tmp.dir1, overwrite=TRUE) # Copy "homo_sapiens.brain.svg" file into 'tmp.dir1'

Query the above aSVG with feature and species keywords, and return the resulting matches in a data.frame.

feature.df <- return_feature(feature=c('frontal cortex', 'prefrontal cortex'), species=c('homo sapiens', 'brain'), dir=tmp.dir1, remote=FALSE, keywords.any=FALSE)
feature.df

Subsequently, create a character vector of new feature identifiers corresponding to each of the returned features.

Sample code that creates new feature names and stores them in a character vector.

f.new <- c('prefrontalCortex', 'frontalCortex')

Similarly, if the stroke (outline thickness) or color need to update, make vectors respectively and make sure each entry corresponds to each returned feature.

s.new <- c('0.05', '0.1') # New strokes.
c.new <- c('red', 'green') # New colors.

Next, new features, strokes, and colors are added to the feature data.frame as three columns with the names featureNew, strokeNew, and colorNew respectively. The three column names are used by the update_feature function to look up new entries.

feature.df.new <- cbind(featureNew=f.new, strokeNew=s.new, colorNew=c.new, feature.df)
feature.df.new

Finally, the features, strokes, and colors are updated in the aSVG file(s) located in the tmp.dir1 directory.

update_feature(df.new=feature.df.new, dir=tmp.dir1)


10 Version Informaion

sessionInfo()
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] GEOquery_2.60.0             ExpressionAtlas_1.20.0     
##  [3] xml2_1.3.2                  limma_3.48.0               
##  [5] SummarizedExperiment_1.22.0 Biobase_2.52.0             
##  [7] GenomicRanges_1.44.0        GenomeInfoDb_1.28.0        
##  [9] IRanges_2.26.0              S4Vectors_0.30.0           
## [11] BiocGenerics_0.38.0         MatrixGenerics_1.4.0       
## [13] matrixStats_0.58.0          spatialHeatmap_1.2.0       
## [15] knitr_1.33                  BiocStyle_2.20.0           
## 
## loaded via a namespace (and not attached):
##   [1] rols_2.20.0            backports_1.2.1        Hmisc_4.5-0           
##   [4] av_0.6.0               BiocFileCache_2.0.0    igraph_1.2.6          
##   [7] lazyeval_0.2.2         shinydashboard_0.7.1   splines_4.1.0         
##  [10] BiocParallel_1.26.0    ggplot2_3.3.3          digest_0.6.27         
##  [13] foreach_1.5.1          htmltools_0.5.1.1      magick_2.7.2          
##  [16] GO.db_3.13.0           fansi_0.4.2            magrittr_2.0.1        
##  [19] checkmate_2.0.0        memoise_2.0.0          cluster_2.1.2         
##  [22] doParallel_1.0.16      readr_1.4.0            fastcluster_1.1.25    
##  [25] Biostrings_2.60.0      annotate_1.70.0        prettyunits_1.1.1     
##  [28] jpeg_0.1-8.1           colorspace_2.0-1       blob_1.2.1            
##  [31] rappdirs_0.3.3         xfun_0.23              dplyr_1.0.6           
##  [34] crayon_1.4.1           RCurl_1.98-1.3         jsonlite_1.7.2        
##  [37] genefilter_1.74.0      impute_1.66.0          survival_3.2-11       
##  [40] iterators_1.0.13       glue_1.4.2             gtable_0.3.0          
##  [43] zlibbioc_1.38.0        XVector_0.32.0         DelayedArray_0.18.0   
##  [46] Rhdf5lib_1.14.0        HDF5Array_1.20.0       scales_1.1.1          
##  [49] DBI_1.1.1              edgeR_3.34.0           Rcpp_1.0.6            
##  [52] progress_1.2.2         viridisLite_0.4.0      xtable_1.8-4          
##  [55] htmlTable_2.2.1        gridGraphics_0.5-1     flashClust_1.01-2     
##  [58] foreign_0.8-81         bit_4.0.4              preprocessCore_1.54.0 
##  [61] Formula_1.2-4          rsvg_2.1.2             htmlwidgets_1.5.3     
##  [64] httr_1.4.2             gplots_3.1.1           RColorBrewer_1.1-2    
##  [67] ellipsis_0.3.2         farver_2.1.0           pkgconfig_2.0.3       
##  [70] XML_3.99-0.6           nnet_7.3-16            sass_0.4.0            
##  [73] dbplyr_2.1.1           locfit_1.5-9.4         utf8_1.2.1            
##  [76] dynamicTreeCut_1.63-1  labeling_0.4.2         later_1.2.0           
##  [79] ggplotify_0.0.7        tidyselect_1.1.1       rlang_0.4.11          
##  [82] AnnotationDbi_1.54.0   visNetwork_2.0.9       munsell_0.5.0         
##  [85] tools_4.1.0            cachem_1.0.5           generics_0.1.0        
##  [88] RSQLite_2.2.7          evaluate_0.14          stringr_1.4.0         
##  [91] fastmap_1.1.0          ggdendro_0.1.22        yaml_2.2.1            
##  [94] bit64_4.0.5            caTools_1.18.2         purrr_0.3.4           
##  [97] KEGGREST_1.32.0        mime_0.10              compiler_4.1.0        
## [100] rstudioapi_0.13        plotly_4.9.3           filelock_1.0.2        
## [103] curl_4.3.1             png_0.1-7              tibble_3.1.2          
## [106] geneplotter_1.70.0     bslib_0.2.5.1          stringi_1.6.2         
## [109] highr_0.9              lattice_0.20-44        Matrix_1.3-3          
## [112] vctrs_0.3.8            pillar_1.6.1           lifecycle_1.0.0       
## [115] rhdf5filters_1.4.0     BiocManager_1.30.15    jquerylib_0.1.4       
## [118] data.table_1.14.0      bitops_1.0-7           grImport_0.9-3        
## [121] httpuv_1.6.1           R6_2.5.0               latticeExtra_0.6-29   
## [124] promises_1.2.0.1       bookdown_0.22          KernSmooth_2.23-20    
## [127] gridExtra_2.3          codetools_0.2-18       MASS_7.3-54           
## [130] gtools_3.8.2           assertthat_0.2.1       rhdf5_2.36.0          
## [133] DESeq2_1.32.0          withr_2.4.2            GenomeInfoDbData_1.2.6
## [136] hms_1.1.0              grid_4.1.0             rpart_4.1-15          
## [139] tidyr_1.1.3            rmarkdown_2.8          rvcheck_0.1.8         
## [142] shiny_1.6.0            WGCNA_1.70-3           base64enc_0.1-3

11 Funding

This project has been funded by NSF awards: PGRP-1546879, PGRP-1810468, PGRP-1936492.

12 References

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