Package: geneplotter 1.91.0
Bioconductor Package Maintainer
geneplotter: Graphics related functions for Bioconductor
Functions for plotting genomic data
Authors:
geneplotter_1.91.0.tar.gz
geneplotter_1.91.0.zip(r-4.7)geneplotter_1.91.0.zip(r-4.6)geneplotter_1.91.0.zip(r-4.5)
geneplotter_1.91.0.tgz(r-4.6-any)geneplotter_1.91.0.tgz(r-4.5-any)
geneplotter_1.91.0.tar.gz(r-4.7-any)geneplotter_1.91.0.tar.gz(r-4.6-any)
geneplotter_1.91.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
geneplotter/json (API)
NEWS
| # Install 'geneplotter' in R: |
| install.packages('geneplotter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- expressionSet133a - A small dataset for testing
- IMCAEntrezLink - A function to plot a graph colored by expression data
On BioConductor:geneplotter-1.91.0(bioc 3.24)geneplotter-1.90.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:5175c4c91d. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 215 | ||
| linux-devel-x86_64 | NOTE | 246 | ||
| source / vignettes | OK | 276 | ||
| linux-release-x86_64 | NOTE | 286 | ||
| macos-release-arm64 | NOTE | 175 | ||
| macos-oldrel-arm64 | NOTE | 207 | ||
| windows-devel | NOTE | 191 | ||
| windows-release | NOTE | 214 | ||
| windows-oldrel | NOTE | 183 | ||
| wasm-release | OK | 173 |
Exports:alongChromcColorcloseHtmlPagecPlotcScaledChip.colorsGetColorgreenred.colorsgroupedHeatmaphistStackimageMapmake.chromOrdMakesensemultidensitymultiecdfopenHtmlPageplotChrplotExpressionGraphplotMAsaveepssavepdfsavepngsavetiff
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsgluehttrIRangesjsonliteKEGGRESTlatticelifecyclememoisemimeopensslpkgconfigpngR6RColorBrewerrlangRSQLiteS4VectorsSeqinfosysvctrsXMLxtableXVector
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 |
