Package: EnrichedHeatmap 1.43.0
Zuguang Gu
EnrichedHeatmap: Making Enriched Heatmaps
Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.
Authors:
EnrichedHeatmap_1.43.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EnrichedHeatmap/json (API)
| # Install 'EnrichedHeatmap' in R: |
| install.packages('EnrichedHeatmap', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jokergoo/enrichedheatmap/issues
On BioConductor:EnrichedHeatmap-1.43.0(bioc 3.24)EnrichedHeatmap-1.42.0(bioc 3.23)
softwarevisualizationsequencinggenomeannotationcoveragecpp
Last updated from:2d9b9e62a1. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 169 | ||
| linux-devel-arm64 | NOTE | 615 | ||
| linux-devel-x86_64 | NOTE | 230 | ||
| source / vignettes | OK | 268 | ||
| linux-release-arm64 | NOTE | 202 | ||
| linux-release-x86_64 | NOTE | 236 | ||
| macos-release-arm64 | NOTE | 266 | ||
| macos-release-x86_64 | NOTE | 493 | ||
| macos-oldrel-arm64 | NOTE | 159 | ||
| macos-oldrel-x86_64 | NOTE | 301 | ||
| windows-devel | NOTE | 170 | ||
| windows-release | NOTE | 236 | ||
| windows-oldrel | NOTE | 155 | ||
| wasm-release | OK | 151 |
Exports:[.normalizedMatrixanno_enrichedas.normalizedMatrixcopyAttrdefault_smooth_fundiscretizedist_by_closenessenriched_scoreEnrichedHeatmapextract_anno_enrichedfailed_rowsgetSignalsFromListmakeWindowsnormalizeToMatrixprint.normalizedMatrixrbind.normalizedMatrix
Dependencies:BiocGenericscirclizeclueclustercodetoolscolorspaceComplexHeatmapcrayondigestdoParallelforeachgenericsGenomicRangesGetoptLongGlobalOptionsIRangesiteratorslatticelocfitmatrixStatspngRColorBrewerRcpprjsonS4VectorsSeqinfoshape
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Subset normalized matrix by rows | Extract.normalizedMatrix [.normalizedMatrix |
| Annotation Function to Show the Enrichment | anno_enriched |
| Convert a Normal Matrix to a normalizedMatrix Object | as.normalizedMatrix |
| Copy Attributes to Another Object | copyAttr |
| Default Smoothing function | default_smooth_fun |
| Discretize a Continuous Matrix to a Discrete Matrix | discretize |
| Distance by Closeness | dist_by_closeness |
| Enriched Scores | enriched_score |
| Constructor Method for the Enriched Heatmap | EnrichedHeatmap |
| Extarct Enrichment Annotation Graphics as a Separated Plot | extract_anno_enriched |
| Indices of Rows Failed from Smoothing | failed_rows |
| Get Signals from a List | getSignalsFromList |
| Split Regions into Windows | makeWindows |
| Normalize Associations between Genomic Signals and Target Regions into a Matrix | normalizeToMatrix |
| Print the Normalized Matrix | print.normalizedMatrix |
| Bind Matrix by Rows | rbind.normalizedMatrix |
