Package: heatmaps 1.31.0

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]>

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heatmaps.pdf |heatmaps.html✨
heatmaps/json (API)
NEWS

# Install 'heatmaps' in R:
install.packages('heatmaps', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.31.0(bioc 3.21)heatmaps-1.30.0(bioc 3.20)

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

visualizationsequencematchingfunctionalgenomics

5.23 score 1 packages 19 scripts 378 downloads 3 mentions 30 exports 58 dependencies

Last updated 23 days agofrom:2ebde801b1. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

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

Dependencies:abindaskpassbase64encBiocGenericsBiostringsbitopsbslibcachemclicrayoncurldigestEBImageevaluatefastmapfftwtoolsfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhtmltoolshtmlwidgetshttrIRangesjpegjquerylibjsonliteKernSmoothknitrlatticelifecyclelocfitMatrixmemoisemimeopensslplotrixpngR6rappdirsRColorBrewerRCurlrlangrmarkdownS4VectorssasssystifftinytexUCSC.utilsxfunXVectoryamlzlibbioc

heatmaps vignette

Malcolm Perry

Rendered fromheatmaps.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2017-04-23
Started: 2017-04-23

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