Package: EnrichedHeatmap 1.37.0
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_1.37.0.tar.gz
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EnrichedHeatmap.pdf |EnrichedHeatmap.html✨
EnrichedHeatmap/json (API)
NEWS
| # 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-1.37.0(bioc 3.21)EnrichedHeatmap-1.36.0(bioc 3.20)
softwarevisualizationsequencinggenomeannotationcoverage
Last updated 25 days agofrom:6e3469a474. Checks:OK: 3 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 08 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 08 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 08 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 08 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 08 2024 |
| R-4.4-mac-aarch64 | OK | Nov 08 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 08 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 08 2024 |
| R-4.3-mac-aarch64 | OK | Nov 08 2024 |
Exports:[.normalizedMatrixanno_enrichedas.normalizedMatrixcopyAttrdefault_smooth_fundiscretizedist_by_closenessenriched_scoreEnrichedHeatmapextract_anno_enrichedfailed_rowsgetSignalsFromListmakeWindowsnormalizeToMatrixprint.normalizedMatrixrbind.normalizedMatrix
Dependencies:askpassBiocGenericscirclizeclueclustercodetoolscolorspaceComplexHeatmapcrayoncurldigestdoParallelforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongGlobalOptionshttrIRangesiteratorsjsonlitelatticelocfitmatrixStatsmimeopensslpngR6RColorBrewerRcpprjsonS4VectorsshapesysUCSC.utilsXVectorzlibbioc
Make Enriched Heatmaps
Rendered fromEnrichedHeatmap.Rmdusingknitr::rmarkdownon Nov 08 2024.Last update: 2023-03-19
Started: 2015-09-28
Visualize Categorical Signals
Rendered fromvisualize_categorical_signals_wrapper.Rmdusingknitr::rmarkdownon Nov 08 2024.Last update: 2023-03-19
Started: 2018-03-13
Compare row ordering methods
Rendered fromrow_odering.Rmdusingknitr::rmarkdownon Nov 08 2024.Last update: 2023-03-19
Started: 2017-10-15
Visualize Comprehensive Associations in Roadmap dataset
Rendered fromroadmap.Rmdusingknitr::rmarkdownon Nov 08 2024.Last update: 2023-03-19
Started: 2017-10-16
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 |
