iSEE {iSEE} | R Documentation |
Interactive and reproducible visualization of data contained in a SummarizedExperiment object, using a Shiny interface.
iSEE( se, initial = NULL, extra = NULL, redDimArgs = NULL, colDataArgs = NULL, featAssayArgs = NULL, rowStatArgs = NULL, rowDataArgs = NULL, sampAssayArgs = NULL, colStatArgs = NULL, customDataArgs = NULL, customStatArgs = NULL, heatMapArgs = NULL, redDimMax = 5, colDataMax = 5, featAssayMax = 5, rowStatMax = 5, rowDataMax = 5, sampAssayMax = 5, colStatMax = 5, customDataMax = 5, customStatMax = 5, heatMapMax = 5, initialPanels = NULL, annotFun = NULL, customDataFun = NULL, customStatFun = NULL, customSendAll = FALSE, colormap = ExperimentColorMap(), landingPage = createLandingPage(), tour = NULL, appTitle = NULL, runLocal = TRUE, voice = FALSE, bugs = FALSE, ... )
se |
An object that is coercible to SingleCellExperiment.
If missing, an app is launched with a landing page generated by the |
initial |
A list of Panel objects specifying the initial state of the app. The order of panels determines the sequence in which they are laid out in the interface. Defaults to one instance of each panel class available from iSEE. |
extra |
A list of additional Panel objects that might be added after the app has started. Defaults to one instance of each panel class available from iSEE. |
redDimArgs |
Deprecated, use |
colDataArgs |
Deprecated, use |
featAssayArgs |
Deprecated, use |
rowStatArgs |
Deprecated, use |
rowDataArgs |
Deprecated, use |
sampAssayArgs |
Deprecated, use |
colStatArgs |
Deprecated, use |
customDataArgs |
Deprecated, use |
customStatArgs |
Deprecated, use |
heatMapArgs |
Deprecated, use |
redDimMax |
Deprecated and ignored. |
colDataMax |
Deprecated and ignored. |
featAssayMax |
Deprecated and ignored. |
rowStatMax |
Deprecated and ignored. |
rowDataMax |
Deprecated and ignored. |
sampAssayMax |
Deprecated and ignored. |
colStatMax |
Deprecated and ignored. |
customDataMax |
Deprecated and ignored. |
customStatMax |
Deprecated and ignored. |
heatMapMax |
Deprecated and ignored. |
initialPanels |
Deprecated, use |
annotFun |
Deprecated and ignored. Read the book for the new, more extensible approach for creating custom panels. |
customDataFun |
Deprecated and ignored. Read the book for the new, more extensible approach for creating custom panels. |
customStatFun |
Deprecated and ignored. Read the book for the new, more extensible approach for creating custom panels. |
customSendAll |
Deprecated and ignored. |
colormap |
An ExperimentColorMap object that defines custom colormaps to apply to individual |
landingPage |
A function that renders a landing page when |
tour |
A data.frame with the content of the interactive tour to be displayed after starting up the app. |
appTitle |
A string indicating the title to be displayed in the app.
If not provided, the app displays the version info of |
runLocal |
A logical indicating whether the app is to be run locally or remotely on a server, which determines how documentation will be accessed. |
voice |
A logical indicating whether the voice recognition should be enabled. |
bugs |
Set to |
... |
Further arguments to pass to |
Configuring the initial state of the app is as easy as passing a list of Panel objects to initial
.
Each element represents one panel and is typicall constructed with a command like ReducedDimensionPlot()
.
Panels are filled from left to right in a row-wise manner depending on the available width.
Each panel can be easily customized by modifying the parameters in each object.
The extra
argument should specify Panel classes that might not be shown during initialization
but can be added interactively by the user after the app has started.
The first instance of each new class in extra
will be used as a template when the user adds a new panel of that class.
Note that initial
will automatically be appended to extra
to form the final set of available panels,
so it is not strictly necessary to re-specify instances of those initial panels in extra
.
(unless we want the parameters of newly created panels to be different from those at initialization).
The tour
argument needs to be provided in a form compatible with the format expected by the rintrojs
package.
There should be two columns, element
and intro
, with the former describing the element to highlight and the latter providing some descriptive text.
See https://github.com/carlganz/rintrojs#usage for more information.
By default, categorical data types such as factor and character are limited to 24 levels, beyond which they are coerced to numeric variables for faster plotting.
This limit may be set to a different value as a global option, e.g. options(iSEE.maxlevels=30)
.
The default landing page allows users to upload their own RDS files to initialize the app.
By default, the maximum request size for file uploads defaults to 5MB
(https://shiny.rstudio.com/reference/shiny/0.14/shiny-options.html).
To raise the limit (e.g., 50MB), run options(shiny.maxRequestSize=50*1024^2)
.
A Shiny app object is returned for interactive data exploration of se
,
either by simply printing the object or by explicitly running it with runApp
.
Rue-Albrecht K, Marini F, Soneson C, Lun ATL. iSEE: Interactive SummarizedExperiment Explorer F1000Research 7.
Javascript code for bugs
was based on https://github.com/Auz/Bug.
library(scRNAseq) # Example data ---- sce <- ReprocessedAllenData(assays="tophat_counts") class(sce) library(scater) sce <- logNormCounts(sce, exprs_values="tophat_counts") sce <- runPCA(sce, ncomponents=4) sce <- runTSNE(sce) rowData(sce)$ave_count <- rowMeans(assay(sce, "tophat_counts")) rowData(sce)$n_cells <- rowSums(assay(sce, "tophat_counts") > 0) sce # launch the app itself ---- app <- iSEE(sce) if (interactive()) { shiny::runApp(app, port=1234) }