Package: plotgardener 1.13.0

Nicole Kramer

plotgardener: Coordinate-Based Genomic Visualization Package for R

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

Authors:Nicole Kramer [aut, cre], Eric S. Davis [aut], Craig Wenger [aut], Sarah Parker [ctb], Erika Deoudes [art], Michael Love [ctb], Douglas H. Phanstiel [aut, cre, cph]

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

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

Peer review:

Bug tracker:https://github.com/phanstiellab/plotgardener/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:plotgardener-1.13.0(bioc 3.21)plotgardener-1.12.0(bioc 3.20)

visualizationgenomeannotationfunctionalgenomicsgenomeassemblyhic

10.20 score 301 stars 3 packages 161 scripts 434 downloads 54 exports 90 dependencies

Last updated 21 days agofrom:bc6f00630e. Checks:OK: 1 NOTE: 1 WARNING: 4 ERROR: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64ERRORNov 19 2024
R-4.5-linux-x86_64NOTENov 19 2024
R-4.4-win-x86_64ERRORNov 19 2024
R-4.4-mac-x86_64WARNINGNov 19 2024
R-4.4-mac-aarch64WARNINGNov 19 2024
R-4.3-win-x86_64ERRORNov 19 2024
R-4.3-mac-x86_64WARNINGNov 19 2024
R-4.3-mac-aarch64WARNINGNov 19 2024

Exports:annoDomainsannoGenomeLabelannoHeatmapLegendannoHighlightannoPixelsannoSegmentsannoTextannoXaxisannoYaxisannoZoomLinesassemblyccalcSignalRangecolorbydefaultPackagesgenomesmapColorspageCreatepageGuideHidepageGuideHorizontalpageGuideShowpageGuideVerticalpageLayoutColpageLayoutRowpagePlotPlacepagePlotRemovepgParamsplotCircleplotGenesplotGenomeLabelplotGGplotHicRectangleplotHicSquareplotHicTriangleplotIdeogramplotLegendplotManhattanplotMultiSignalplotPairsplotPairsArchesplotPolygonplotRangesplotRasterplotRectplotSegmentsplotSignalplotTextplotTranscriptsreadBigwigreadCoolreadCoolBpResolutionsreadCoolChromsreadCoolNormsreadHic

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydigestdplyrfansifarverformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggplotifygluegridGraphicsgtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrangespurrrR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraystrawrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlyulab.utilszlibbioc

Introduction to plotgardener

Nicole Kramer, Eric S. Davis, Craig Wenger, Sarah Parker, Erika Deoudes, Michael Love, Douglas H. Phanstiel

Rendered fromintroduction_to_plotgardener.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-08-04
Started: 2021-08-19

Readme and manuals

Help Manual

Help pageTopics
Check for .(m)cool file and contents.checkCool
Error checking function for .(m)cool files.checkCoolErrors
Determine best resolution for size of region for .(m)cool files.coolAutoResolution
Add (alt)chromstart and (alt)chromend for NULL (alt)chrom region of .(m)cool files.coolRegion
Read in data for a bin chunk.pullBinChunks
Annotate domains in a Hi-C plotannoDomains
Annotate genomic coordinates along the x or y-axis of a plotannoGenomeLabel
Add a color scale legend for heatmap-style plotsannoHeatmapLegend
Annotates a highlight box around a specified genomic region of a plotannoHighlight
Annotate pixels in a Hi-C plotannoPixels
Annotates a line segment within a plotannoSegments
Annotates text within a plotannoText
Add an x-axis to a plotannoXaxis
Add a y-axis to a plotannoYaxis
Annotates zoom lines for a specified genomic region of a plotannoZoomLines
Make a 'assembly' object for alternate TxDb, OrgDb,and BSgenome genomic annotation packagesassembly
Combine multiple pgParams objects into a vectorc
Calculate a score range for multiple signalscalcSignalRange
Handle plotgardener color scaling parameterscolorby
Display the default genomic annotation packages associated with a genome builddefaultPackages
Display the included available default genome assembliesgenomes
Maps a numeric or character vector to a color palette and returns the vector of colorsmapColors
Create a page for a plotgardener layoutpageCreate
Remove guides from a plotgardener pagepageGuideHide
Draw a horizontal guideline at a specified y-coordinate on a plotgardener pagepageGuideHorizontal
Reshow guides drawn with 'pageCreate', 'pageGuideHorizontal', and 'pageGuideVertical'pageGuideShow
Draw a vertical guideline at a specified x-coordinate on a plotgardener pagepageGuideVertical
Generate column positions for a number of plot elements with a specified width and space between thempageLayoutCol
Generate row positions for a number of plot elements with a specified height and space between thempageLayoutRow
Place a plot that has been previously created but not drawnpagePlotPlace
Remove plotgardener plots and annotationspagePlotRemove
pgParams: plotgardener parameters objectpgParams
Plot a circle within a plotgardener layoutplotCircle
plotgardener: Coordinate-based Genomic Visualization Package for Rplotgardener-package plotgardener
Plot a gene track for a specified genomic regionplotGenes
Plot genomic coordinates along the x or y-axis of a plotgardener plotplotGenomeLabel
Plot a ggplot2 plot, gtable, or grob object in a plotgardener layoutplotGG
Plot a triangular Hi-C interaction matrix in a rectangular formatplotHicRectangle
Plot a Hi-C interaction matrix in a square formatplotHicSquare
Plot a Hi-C interaction matrix in a triangular formatplotHicTriangle
Plot a chromosome ideogram with or without cytobandsplotIdeogram
Plot a legendplotLegend
Plot a Manhattan plotplotManhattan
Plot multiple signal tracks in line with each otherplotMultiSignal
Plot paired-end genomic range elementsplotPairs
Plot paired-end genomic range data in an arch styleplotPairsArches
Plot a polygon within a plotgardener layoutplotPolygon
Plot genomic range elements in a pileup or collapsed formatplotRanges
Plot a raster object within a plotgardener layoutplotRaster
Plot a rectangle within a plotgardener layoutplotRect
Draw a line segment within a plotgardener layoutplotSegments
Plot any kind of signal track data for a single chromosomeplotSignal
Plot text within a plotgardener layoutplotText
Plot gene transcripts in a pileup style for a single chromosomeplotTranscripts
Read a bigWig file and return it as a data framereadBigwig
Read a .(m)cool file and return Hi-C data as a dataframereadCool
Read basepair resolutions from an .(m)cool filereadCoolBpResolutions
Read chromosomes included in .(m)cool filesreadCoolChroms
Read normalizations included in .(m)cool filesreadCoolNorms
Read a .hic file and return Hi-C data as a dataframereadHic