spatialHeatmap
This is the development version of spatialHeatmap; for the stable release version, see spatialHeatmap.
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
Bioconductor version: Development (3.24)
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("spatialHeatmap")):Jianhai Zhang, Le Zhang, Jordan Hayes, Brendan Gongol, Alexander Borowsky, Julia Bailey-Serres, Thomas Girke. spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions. doi:10.18129/B9.bioc.spatialHeatmap, R package version 2.19.2, https://bioconductor.org/packages/spatialHeatmap.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| (B) Co-visualizing Bulk and Single-cell Assay Data | HTML | R Script |
| (C) Creating Custom Annotated SVGs | HTML | R Script |
| (A) Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions | 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 | 2.19.2 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0) |
| 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 |
See More
| Suggests | AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, bluster, cachem, DESeq2, dendextend, DT, dynamicTreeCut, DelayedArray, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, jsonlite, 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, rappdirs, RUnit, Rtsne, rhdf5, scater, scrapper, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spatialHeatmap_2.19.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | spatialHeatmap_2.19.2.tgz |
| macOS Binary (sonoma-arm64) | spatialHeatmap_2.19.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spatialHeatmap |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spatialHeatmap |
| Package Short Url | https://bioconductor.org/packages/spatialHeatmap/ |
| Package Downloads Report | Download Stats |