This package is for version 3.15 of Bioconductor;
for the stable, up-to-date release version, see
spatialHeatmap.
spatialHeatmap
Bioconductor version: 3.15
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 ucr.edu>
Citation (from within R, enter citation("spatialHeatmap")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spatialHeatmap")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("spatialHeatmap")
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Network Graphs
HTML
R Script
Details
biocViews
ATACSeq,
CellBasedAssays,
CellBiology,
Clustering,
DNASeq,
DataRepresentation,
GeneExpression,
GeneTarget,
GraphAndNetwork,
Microarray,
Network,
Sequencing,
SingleCell,
Software,
Spatial,
TissueMicroarray,
Visualization
Version
2.2.0
In Bioconductor since
BioC 3.12 (R-4.0) (3.5 years)
License
Artistic-2.0
Depends
R (>= 3.5.0)
Imports
av,
BiocParallel,
BiocFileCache, data.table,
DESeq2,
distinct,
edgeR, WGCNA, flashClust, htmlwidgets,
genefilter, ggplot2, ggdendro, grImport, grid, gridExtra, gplots, igraph,
HDF5Array,
limma, methods, magick, Matrix, rsvg, shiny, dynamicTreeCut, grDevices, graphics, ggplotify, parallel, plotly, pROC,
rols, rappdirs, reshape2,
scater,
scuttle,
scran, stats,
SummarizedExperiment,
SingleCellExperiment, shinydashboard,
S4Vectors, utils, visNetwork, UpSetR, xml2, yaml
System Requirements
See More
Suggests
knitr, rmarkdown,
BiocStyle,
BiocSingular, RUnit,
BiocGenerics,
ExpressionAtlas, DT,
Biobase,
GEOquery, shinyWidgets, shinyjs, htmltools, shinyBS, sortable
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/spatialHeatmap
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/spatialHeatmap