spatialHeatmap

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.

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 ucr.edu>

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")

 

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

Details

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
LinkingTo
Suggests	av, knitr, rmarkdown, BiocStyle, BiocSingular, RUnit, BiocGenerics, DESeq2, distinct, HDF5Array, kableExtra, magick, ExpressionAtlas, DT, Biobase, GEOquery, pROC, rols, shinyWidgets, shinyjs, htmltools, shinyBS, sortable
SystemRequirements
Enhances
URL	https://github.com/jianhaizhang/spatialHeatmap
BugReports	https://github.com/jianhaizhang/spatialHeatmap/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	spatialHeatmap_2.4.0.tar.gz
Windows Binary	spatialHeatmap_2.4.0.zip
macOS Binary (x86_64)	spatialHeatmap_2.4.0.tgz
macOS Binary (arm64)	spatialHeatmap_2.4.0.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