Package: heatmaps 1.37.0

Malcolm Perry

heatmaps: Flexible Heatmaps for Functional Genomics and Sequence Features

This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

Authors:Malcolm Perry <[email protected]>

heatmaps_1.37.0.tar.gz
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heatmaps_1.37.0.tgz(r-4.6-any)heatmaps_1.37.0.tgz(r-4.5-any)
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heatmaps_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
heatmaps/json (API)

# Install 'heatmaps' in R:
install.packages('heatmaps', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • hm - Data for man page examples
  • hm2 - Data for man page examples
  • mat - Data for man page examples
  • rle_list - Data for man page examples
  • string_set - Data for man page examples
  • tata_pwm - Data for man page examples
  • windows - Data for man page examples

On BioConductor:heatmaps-1.37.0(bioc 3.24)heatmaps-1.36.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualizationsequencematchingfunctionalgenomics

3.98 score 21 scripts 3 mentions 30 exports 49 dependencies

Last updated from:1aa6a5611b. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR222
linux-devel-x86_64WARNING288
source / vignettesERROR357
linux-release-x86_64WARNING286
macos-release-arm64WARNING142
macos-oldrel-arm64WARNING147
windows-develWARNING582
windows-releaseWARNING614
windows-oldrelWARNING644
wasm-releaseOK186

Exports:coordscoords<-CoverageHeatmapdefault_colorgetScaleHeatmapheatmapOptionsimageimage<-labellabel<-metadatametadata<-nseqnseq<-PatternHeatmapplot_clustersplot_legendplotHeatmapplotHeatmapListplotHeatmapMetaplotPatternDensityMapPWMScanHeatmaprevscalescale<-smoothHeatmapwidthxmym

Dependencies:abindbase64encBiocGenericsBiostringsbitopsbslibcachemclicrayondigestEBImageevaluatefastmapfftwtoolsfontawesomefsgenericsGenomicRangeshighrhtmltoolshtmlwidgetsIRangesjpegjquerylibjsonliteKernSmoothknitrlatticelifecyclelocfitMatrixmemoisemimeplotrixpngR6rappdirsRColorBrewerRCurlrlangrmarkdownS4VectorssassSeqinfotifftinytexxfunXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Return or set the coords in a Heatmapcoords coords,Heatmap-method coords<- coords<-,Heatmap-method
Generate a Heatmap of coverageCoverageHeatmap CoverageHeatmap,GenomicRanges,GenomicRanges-method CoverageHeatmap,GenomicRanges,RleList-method
Predifined color palettes from RColorBrewer + Rainbowdefault_color
Make an appropriate scale for a heatmapgetScale
Function to create a heatmap objectHeatmap
An S4 class to represent a heatmapHeatmap-class
Data for man page examplesHeatmapExamples hm hm2 mat rle_list string_set tata_pwm windows
Generate default options for a HeatmapheatmapOptions
Return or set the image in a Heatmapimage image,Heatmap-method image<- image<-,Heatmap-method
Return or set the label in a Heatmaplabel label,Heatmap-method label<- label<-,Heatmap-method
Return the number of sequences in a heatmaplength,Heatmap-method
Return or set the metadata in a Heatmapmetadata metadata,Heatmap-method metadata<- metadata<-,Heatmap-method
Return or set nseq in a Heatmapnseq nseq,Heatmap-method nseq<- nseq<-,Heatmap-method
Generate a Heatmap of patterns in DNA sequencePatternHeatmap PatternHeatmap,DNAStringSet,character-method PatternHeatmap,DNAStringSet,matrix-method
Plot partition in a separate panelplot_clusters
Plot a color legend for a heatmapplot_legend
Plot a Heatmap object to the deviceplotHeatmap plotHeatmap,Heatmap-method
Plot a list of heatmapsplotHeatmapList
Plot a Meta-region plot from heatmapsplotHeatmapMeta
Plot heatmaps for several patterns in DNA sequenceplotPatternDensityMap plotPatternDensityMap,DNAStringSet-method
Generate a Heatmap of PWM Scores in DNA sequncePWMScanHeatmap PWMScanHeatmap,DNAStringSet,matrix-method
Reflect a heatmap in the x axisrev,Heatmap-method
Return or set the scale in a Heatmapscale scale,Heatmap-method scale<- scale<-,Heatmap-method
Smooth a heatmapsmoothHeatmap smoothHeatmap,Heatmap-method
Return the width of sequence represented in a heatmapwidth,Heatmap-method
Generate co-ordinates for each row of the image matrix of a Heatmapxm xm,Heatmap-method
Generate co-ordinates for each column of the image matrix of a Heatmapym ym,Heatmap-method