Package: geneplotter 1.83.0

Bioconductor Package Maintainer

geneplotter: Graphics related functions for Bioconductor

Functions for plotting genomic data

Authors:Robert Gentleman [aut], Rohit Satyam [ctb], Bioconductor Package Maintainer [cre]

geneplotter_1.83.0.tar.gz
geneplotter_1.83.0.zip(r-4.5)geneplotter_1.83.0.zip(r-4.4)geneplotter_1.83.0.zip(r-4.3)
geneplotter_1.83.0.tgz(r-4.4-any)geneplotter_1.83.0.tgz(r-4.3-any)
geneplotter_1.83.0.tar.gz(r-4.5-noble)geneplotter_1.83.0.tar.gz(r-4.4-noble)
geneplotter_1.83.0.tgz(r-4.4-emscripten)geneplotter_1.83.0.tgz(r-4.3-emscripten)
geneplotter.pdf |geneplotter.html✨
geneplotter/json (API)
NEWS

# Install 'geneplotter' in R:

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

Datasets:

IMCAEntrezLink - A function to plot a graph colored by expression data
expressionSet133a - A small dataset for testing

On BioConductor:geneplotter-1.83.0(bioc 3.20)geneplotter-1.82.0(bioc 3.19)

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

bioconductor-package

23 exports 3.76 score 43 dependencies 12 dependents 14 mentions

Last updated 2 months agofrom:7f7fe9bde7

Exports:alongChrom cColor closeHtmlPage cPlot cScale dChip.colors GetColor greenred.colors groupedHeatmap histStack imageMap make.chromOrd Makesense multidensity multiecdf openHtmlPage plotChr plotExpressionGraph plotMA saveeps savepdf savepng savetiff

Dependencies:annotate AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lattice lifecycle memoise mime openssl pkgconfig plogr png R6 RColorBrewer rlang RSQLite S4Vectors sys UCSC.utils vctrs XML xtable XVector zlibbioc

How to Assemble a chromLocation Object

Robert Gentleman, Rohit Satyam

Rendered frombyChroms.Rmdusingknitr::rmarkdownon Jul 03 2024.

Last update: 2023-06-06
Started: 2023-06-06

Visualization of Microarray Data

Rendered fromvisualize.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2013-10-25
Started: 2013-10-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A function for plotting expression data from an ExpressionSet for a given chromosome.	alongChrom buildACMainLabel cullACXPoints dispACXaxis doACCumPlot doACImagePlot doACLocalPlot doACMatPlot emptyACPlot fixACPhysPoints getACClosestPos getACDataEnv getACExprs getACGeneSyms getACPlotLabs getACStrandVals highlightACDups limitACXRange scaleACData
Create an amplicon plot	amplicon.plot
A function for marking specific probes on a cPlot.	cColor
A plotting function for chromosomes.	cPlot
A function for mapping chromosome length to a number of points.	cScale
A small dataset for testing	expressionSet133a
A function to get the Red-Blue color scheme used by dChip	dChip.colors GetColor greenred.colors
Heatmap of a matrix with grouped rows and columns	groupedHeatmap
Stacked histogram	histStack
Write an HTML IMG tag together with a MAP image map.	imageMap imageMap,matrix,connection,list,character-method imageMap,matrix-method imageMap-methods
Make a chromOrd object	make.chromOrd
Produce Smoothed Sense/Anti-sense For All Chromosomes	Makesense Makesense,ExpressionSet,character-method Makesense,ExpressionSet,missing-method Makesense,matrix,character-method
Multiple empirical cumulative distribution functions (ecdf) and densities	multidensity multidensity.formula multidensity.list multidensity.matrix multiecdf multiecdf.formula multiecdf.list multiecdf.matrix
Open and close an HTML file for writing.	closeHtmlPage openHtmlPage
Plot Smoothed Sense/Anti-sense of Specified Chromosomes	plotChr
A function to plot a graph colored by expression data	defMapFun getPlotExpressionColors IMCAEntrezLink plotExpressionGraph
Generate an MA plot	plotMA plotMA,data.frame-method plotMA,ExonCountSet-method plotMA-methods
Save the contents of the current graphics device to a file	saveeps savepdf savepng savetiff