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spatialHeatmap

This is the development version of spatialHeatmap; for the stable release version, see spatialHeatmap.

spatialHeatmap


Bioconductor version: Development (3.19)

The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data.

Author: Jianhai Zhang [aut, trl, cre], Le Zhang [aut], Jordan Hayes [aut], Brendan Gongol [aut], Alexander Borowsky [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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
(A) Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions HTML R Script
(B) Co-visualizing Bulk and Single-cell Assay Data HTML R Script
(C) Creating Custom Annotated SVGs HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, Spatial, TissueMicroarray, Visualization
Version 2.9.5
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, gplots, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, scater, scuttle, scran, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2
System Requirements
URL https://github.com/jianhaizhang/spatialHeatmap
Bug Reports https://github.com/jianhaizhang/spatialHeatmap/issues
See More
Suggests AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, yaml
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package spatialHeatmap_2.9.5.tar.gz
Windows Binary spatialHeatmap_2.9.5.zip
macOS Binary (x86_64) spatialHeatmap_2.9.5.tgz
macOS Binary (arm64) spatialHeatmap_2.9.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/spatialHeatmap
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spatialHeatmap
Bioc Package Browser https://code.bioconductor.org/browse/spatialHeatmap/
Package Short Url https://bioconductor.org/packages/spatialHeatmap/
Package Downloads Report Download Stats