spatialHeatmap
This is the development version of spatialHeatmap; for the stable release version, see spatialHeatmap.
spatialHeatmap
Bioconductor version: Development (3.18)
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("spatialHeatmap")):
Installation
To install this package, start R (version "4.3") 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")| Co-visualizing spatial heatmaps with single cell embedding plots | HTML | R Script |
| spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Network Graphs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, Spatial, TissueMicroarray, Visualization |
| Version | 2.7.5 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| Imports | data.table, dplyr, edgeR, genefilter, ggplot2, ggdendro, 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 |
| Linking To | |
| Suggests | AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, distinct, dendextend, DT, dynamicTreeCut, flashClust, 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, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, uwot, UpSetR, visNetwork, WGCNA, yaml |
| System Requirements | |
| Enhances | |
| URL | https://github.com/jianhaizhang/spatialHeatmap |
| Bug Reports | https://github.com/jianhaizhang/spatialHeatmap/issues |
See More
| 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_2.7.5.tar.gz |
| Windows Binary | spatialHeatmap_2.7.5.zip |
| macOS Binary (x86_64) | spatialHeatmap_2.7.5.tgz |
| macOS Binary (arm64) | |
| 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 |