Package: ChromHeatMap 1.61.0

Tim F. Rayner

ChromHeatMap: Heat map plotting by genome coordinate

The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.

Authors:Tim F. Rayner

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ChromHeatMap.pdf |ChromHeatMap.html✨
ChromHeatMap/json (API)

# Install 'ChromHeatMap' in R:

install.packages('ChromHeatMap', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

ALLs.chr22 - Chromosome 22 subset of ALL data for ALL1/AF4 and E2A/PBX1
chrdata - The ALLs.chr22 ExpressionSet, reformatted as a ChrStrandData object
cytobands - Cytoband location information
stains - Cytoband display information

On BioConductor:ChromHeatMap-1.61.0(bioc 3.21)ChromHeatMap-1.60.0(bioc 3.20)

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

visualization

3.30 score 311 downloads 1 mentions 8 exports 70 dependencies

Last updated 2 months agofrom:31693e702f. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:chrHeatMap chrNames createChrMatrix drawMapDendro grabChrMapProbes makeChrStrandData makeRangedDataList plotChrMap

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils vctrs XML xtable XVector yaml zlibbioc

Plotting expression data with ChromHeatMap

Rendered fromChromHeatMap.Rnwusingutils::Sweaveon Nov 29 2024.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Chromosome 22 subset of ALL data for ALL1/AF4 and E2A/PBX1	ALLs.chr22
The ALLs.chr22 ExpressionSet, reformatted as a ChrStrandData object	chrdata
Plot ChrStrandMatrix objects as heat maps along a chromosome	chrHeatMap
Class containing a mapping between plot location and probe or gene identifier.	ChrMapPlot ChrMapPlot-class class:ChrMapPlot show,ChrMapPlot-method summary,ChrMapPlot-method
Retrieve chromosome names from an object.	chrNames
Class to contain data associated with chromosome coordinates across a whole genome.	annotation,ChrStrandData-method chrNames,ChrStrandData-method ChrStrandData ChrStrandData-class class:ChrStrandData sampleNames,ChrStrandData-method show,ChrStrandData-method summary,ChrStrandData-method
Class to contain data associated with genome locations for a specific chromosome.	chrNames,ChrStrandMatrix-method ChrStrandMatrix ChrStrandMatrix-class class:ChrStrandMatrix exprs,ChrStrandMatrix-method featureNames,ChrStrandMatrix-method sampleNames,ChrStrandMatrix-method show,ChrStrandMatrix-method strandName,ChrStrandMatrix-method summary,ChrStrandMatrix-method
Generate chromosome-based subset matrices from the mapped data structures generated by makeChrStrandData	createChrMatrix
Cytoband location information	cytobands
Draw a heatmap and dendrogram for a strand-specific data matrix generated by createChrMatrix	drawMapDendro
Identify the probes or genes plotted using plotChrMap	grabChrMapProbes
Map a data matrix onto chromosome coordinates	makeChrStrandData
Map a data matrix onto chromosome coordinates	makeChrStrandData,ExpressionSet-method makeChrStrandData,matrix-method makeChrStrandData-methods
Plot expression data as tracks in the UCSC genome browser	makeRangedDataList
Plot data as an annotated heat map along a chromosome	plotChrMap
Cytoband display information	stains
Retrieve strand information from a ChrStrandMatrix object.	strandName