spatialHeatmap
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
Bioconductor version: 3.23 · Package version: 2.18.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spatialHeatmap")Details
| Maintainer | Jianhai Zhang <jzhan067@ucr.edu> |
| 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] |
| License | Artistic-2.0 |
| URL | https://spatialheatmap.org, https://github.com/jianhaizhang/spatialHeatmap |
| Bug Reports | https://github.com/jianhaizhang/spatialHeatmap/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ATACSeq, CellBasedAssays, CellBiology, Clustering, DNASeq, DataRepresentation, GeneExpression, GeneTarget, GraphAndNetwork, Microarray, Network, Sequencing, SingleCell, Software, Spatial, TissueMicroarray, Visualization |
| Package Short Url | https://bioconductor.org/packages/spatialHeatmap/ |
Citation
From within R, enter 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 2.18.2, https://bioconductor.org/packages/spatialHeatmap.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
- spatialHeatmap: Co-visualizing Bulk and Single-cell Assay Data
- Creating Custom Annotated SVGs
Download
Follow the installation instructions to use this package in your R session.
| Source package | spatialHeatmap_2.18.2.tar.gz |
| macOS binary (arm64) | spatialHeatmap_2.18.1.tgz |
Dependencies
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
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