Introduction | Installation | Create a heatmap object | Manual column ordering | Constructing from a SummarizedExperiment | Plot components | Compose and customize with patchwork | Subsetting and reclustering | Replacing assay values | Session information
Package: SummarizedHeatmap 0.99.0
Bradley Blaser
SummarizedHeatmap: Heatmaps for SummarizedExperiment Objects
Represents a heatmap as a SummarizedExperiment-derived object, holding a single assay together with its row and column annotations and any hierarchical clustering. Assay values, annotations, display order, and dendrograms stay synchronized as the object is subsetted or reclustered, so a heatmap's components cannot drift out of step with each other. Each visual component (the main heatmap, annotation strips, dendrograms) is returned as an ordinary ggplot2 plot, and these can be composed, laid out, and customized using patchwork.
Authors:
SummarizedHeatmap_0.99.0.tar.gz
SummarizedHeatmap_0.99.0.zip(r-4.7-any)SummarizedHeatmap_0.99.0.zip(r-4.6-any)SummarizedHeatmap_0.99.0.zip(r-4.5-any)
SummarizedHeatmap_0.99.0.tgz(r-4.6-any)SummarizedHeatmap_0.99.0.tgz(r-4.5-any)
SummarizedHeatmap_0.99.0.tar.gz(r-4.7-any)SummarizedHeatmap_0.99.0.tar.gz(r-4.6-any)
SummarizedHeatmap_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SummarizedHeatmap/json (API)
| # Install 'SummarizedHeatmap' in R: |
| install.packages('SummarizedHeatmap', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/blaserlab/summarizedheatmap/issues
softwareclusteringvisualization
Last updated from:fc974b60c8. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 182 | ||
| linux-devel | OK | 239 | ||
| source / vignettes | OK | 201 | ||
| linux-release | OK | 199 | ||
| macos-release | OK | 168 | ||
| macos-oldrel | OK | 180 | ||
| windows-devel | OK | 201 | ||
| windows-release | OK | 200 | ||
| windows-oldrel | OK | 185 | ||
| wasm-release | OK | 109 |
Exports:assay<-assays<-clusterColsclusterHeatmapclusterRowscolDendrocolOrderplotColDataplotColDendroplotHeatmapplotHeatmapMainplotRowDataplotRowDendrorowDendrorowOrderSummarizedHeatmap
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayfarvergenericsGenomicRangesggdendroggplot2gluegtableIRangesisobandlabelinglatticelifecycleMASSMatrixMatrixGenericsmatrixStatspatchworkR6RColorBrewerrlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraySummarizedExperimentvctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SummarizedHeatmap | SummarizedHeatmap-package |
| Subset a SummarizedHeatmap | [,SummarizedHeatmap,ANY,ANY,ANY-method |
| Replace the assay of a SummarizedHeatmap | assay-set-SummarizedHeatmap assay<-,SummarizedHeatmap,character-method assay<-,SummarizedHeatmap,missing-method assay<-,SummarizedHeatmap,numeric-method |
| Replace the assays of a SummarizedHeatmap | assays-set-SummarizedHeatmap assays<-,SummarizedHeatmap,list-method assays<-,SummarizedHeatmap,SimpleList-method |
| Cluster columns | clusterCols |
| Cluster rows and columns | clusterHeatmap |
| Cluster rows | clusterRows |
| Access stored column dendrogram | colDendro colDendro,SummarizedHeatmap-method |
| Access column display order | colOrder colOrder,SummarizedHeatmap-method |
| Plot column annotations | plotColData |
| Plot the stored column dendrogram | plotColDendro |
| Compose a complete heatmap with patchwork | plotHeatmap |
| Plot the assay as a ggplot heatmap | plotHeatmapMain |
| Plot row annotations | plotRowData |
| Plot the stored row dendrogram | plotRowDendro |
| Access stored row dendrogram | rowDendro rowDendro,SummarizedHeatmap-method |
| Access row display order | rowOrder rowOrder,SummarizedHeatmap-method |
| Display a concise summary of a SummarizedHeatmap | show,SummarizedHeatmap-method |
| Create a SummarizedHeatmap | SummarizedHeatmap |
| SummarizedHeatmap class | SummarizedHeatmap-class |
