DOI: 10.18129/B9.bioc.spatialHeatmap  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see spatialHeatmap.


Bioconductor version: 3.16

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.

Author: Jianhai Zhang [aut, trl, cre], Jordan Hayes [aut], Le Zhang [aut], Bing Yang [aut], Wolf Frommer [aut], Julia Bailey-Serres [aut], Thomas Girke [aut]

Maintainer: Jianhai Zhang <jzhan067 at>

Citation (from within R, enter citation("spatialHeatmap")):


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HTML R Script Co-visualizing spatial heatmaps with single cell embedding plots
HTML R Script spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Network Graphs
PDF   Reference Manual
Text   NEWS


biocViews ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, Spatial, TissueMicroarray, Visualization
Version 2.4.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports BiocParallel, BiocFileCache, data.table, dplyr, edgeR, WGCNA, flashClust, htmlwidgets, genefilter, ggplot2, ggdendro, grImport, grid, gridExtra, gplots, igraph, limma, methods, Matrix, rsvg, shiny, dynamicTreeCut, grDevices, graphics, ggplotify, parallel, plotly, rappdirs, reshape2, scater, scuttle, scran, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, tibble, utils, visNetwork, UpSetR, xml2, yaml
Suggests av, knitr, rmarkdown, BiocStyle, BiocSingular, RUnit, BiocGenerics, DESeq2, distinct, HDF5Array, kableExtra, magick, ExpressionAtlas, DT, Biobase, GEOquery, pROC, rols, shinyWidgets, shinyjs, htmltools, shinyBS, sortable
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