Package: geneplotter 1.85.0
Bioconductor Package Maintainer
geneplotter: Graphics related functions for Bioconductor
Functions for plotting genomic data
Authors:
geneplotter_1.85.0.tar.gz
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geneplotter_1.85.0.tgz(r-4.4-any)geneplotter_1.85.0.tgz(r-4.3-any)
geneplotter_1.85.0.tar.gz(r-4.5-noble)geneplotter_1.85.0.tar.gz(r-4.4-noble)
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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')) |
- 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.
Last updated 20 days agofrom:fac451a655. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:alongChromcColorcloseHtmlPagecPlotcScaledChip.colorsGetColorgreenred.colorsgroupedHeatmaphistStackimageMapmake.chromOrdMakesensemultidensitymultiecdfopenHtmlPageplotChrplotExpressionGraphplotMAsaveepssavepdfsavepngsavetiff
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlatticelifecyclememoisemimeopensslpkgconfigplogrpngR6RColorBrewerrlangRSQLiteS4VectorssysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
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 |
