spatialHeatmap

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see spatialHeatmap.

spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Bioconductor version: 3.20

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. A description of the project is available here: https://spatialheatmap.org.

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")
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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, Spatial, TissueMicroarray, Visualization

Version 2.12.1

In Bioconductor since BioC 3.12 (R-4.0) (4.5 years)

License Artistic-2.0

Depends R (>= 3.5.0)

Imports data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2

System Requirements

URL https://spatialheatmap.org https://github.com/jianhaizhang/spatialHeatmap

Bug Reports https://github.com/jianhaizhang/spatialHeatmap/issues

Suggests AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, 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, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml

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Package Archives

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

Source Package spatialHeatmap_2.12.1.tar.gz

Windows Binary (x86_64) spatialHeatmap_2.12.1.zip

macOS Binary (x86_64) spatialHeatmap_2.12.1.tgz

macOS Binary (arm64) spatialHeatmap_2.12.1.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

Old Source Packages for BioC 3.20 Source Archive