spatialHeatmap
This is the released version of spatialHeatmap; for the devel version, see spatialHeatmap.
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 |
| (C) Creating Custom Annotated SVGs | 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 | 2.18.2 |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spatialHeatmap_2.18.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | spatialHeatmap_2.18.1.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 3.23 | Source Archive |