Package: plotgardener 1.18.0

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]

# Install 'plotgardener' in R:

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

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

Pkgdown/docs site:https://phanstiellab.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:plotgardener-1.19.0(bioc 3.24)plotgardener-1.18.0(bioc 3.23)

visualization genomeannotation functionalgenomics genomeassembly hic cpp

8.69 score 371 stars 4 packages 8 scripts 718 downloads 54 exports 89 dependencies

Last updated from:aea0b4dba5 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK, 6 WARNING. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	348
linux-devel-arm64	NOTE	584
linux-devel-x86_64	NOTE	733
source / vignettes	OK	601
linux-release-arm64	NOTE	595
linux-release-x86_64	NOTE	720
macos-release-arm64	WARNING	590
macos-release-x86_64	WARNING	793
macos-oldrel-arm64	WARNING	658
macos-oldrel-x86_64	WARNING	1139
windows-devel-arm64	WARNING	752
windows-devel-x86_64	NOTE	658
windows-release-arm64	WARNING	670
windows-release-x86_64	NOTE	591
windows-oldrel-x86_64	NOTE	691
wasm-release	OK	274

Exports:annoDomains annoGenomeLabel annoHeatmapLegend annoHighlight annoPixels annoSegments annoText annoXaxis annoYaxis annoZoomLines assembly c calcSignalRange colorby defaultPackages genomes mapColors pageCreate pageGuideHide pageGuideHorizontal pageGuideShow pageGuideVertical pageLayoutCol pageLayoutRow pagePlotPlace pagePlotRemove pgParams plotCircle plotGenes plotGenomeLabel plotGG plotHicRectangle plotHicSquare plotHicTriangle plotIdeogram plotLegend plotManhattan plotMultiSignal plotPairs plotPairsArches plotPolygon plotRanges plotRaster plotRect plotSegments plotSignal plotText plotTranscripts readBigwig readCool readCoolBpResolutions readCoolChroms readCoolNorms readHic

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO biocmake BiocParallel Biostrings bitops cigarillo cli codetools cpp11 crayon curl data.table DelayedArray digest dir.expiry dplyr farver filelock formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify glue gridGraphics gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig plyranges purrr R6 rappdirs RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray strawr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml yulab.utils

Introduction to plotgardener

Rendered fromintroduction_to_plotgardener.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 plot	annoDomains
Annotate genomic coordinates along the x or y-axis of a plot	annoGenomeLabel
Add a color scale legend for heatmap-style plots	annoHeatmapLegend
Annotates a highlight box around a specified genomic region of a plot	annoHighlight
Annotate pixels in a Hi-C plot	annoPixels
Annotates a line segment within a plot	annoSegments
Annotates text within a plot	annoText
Add an x-axis to a plot	annoXaxis
Add a y-axis to a plot	annoYaxis
Annotates zoom lines for a specified genomic region of a plot	annoZoomLines
Make a 'assembly' object for alternate TxDb, OrgDb,and BSgenome genomic annotation packages	assembly
Combine multiple pgParams objects into a vector	c
Calculate a score range for multiple signals	calcSignalRange
Handle plotgardener color scaling parameters	colorby
Display the default genomic annotation packages associated with a genome build	defaultPackages
Display the included available default genome assemblies	genomes
Maps a numeric or character vector to a color palette and returns the vector of colors	mapColors
Create a page for a plotgardener layout	pageCreate
Remove guides from a plotgardener page	pageGuideHide
Draw a horizontal guideline at a specified y-coordinate on a plotgardener page	pageGuideHorizontal
Reshow guides drawn with 'pageCreate', 'pageGuideHorizontal', and 'pageGuideVertical'	pageGuideShow
Draw a vertical guideline at a specified x-coordinate on a plotgardener page	pageGuideVertical
Generate column positions for a number of plot elements with a specified width and space between them	pageLayoutCol
Generate row positions for a number of plot elements with a specified height and space between them	pageLayoutRow
Place a plot that has been previously created but not drawn	pagePlotPlace
Remove plotgardener plots and annotations	pagePlotRemove
pgParams: plotgardener parameters object	pgParams
Plot a circle within a plotgardener layout	plotCircle
plotgardener: Coordinate-based Genomic Visualization Package for R	plotgardener-package plotgardener
Plot a gene track for a specified genomic region	plotGenes
Plot genomic coordinates along the x or y-axis of a plotgardener plot	plotGenomeLabel
Plot a ggplot2 plot, gtable, or grob object in a plotgardener layout	plotGG
Plot a triangular Hi-C interaction matrix in a rectangular format	plotHicRectangle
Plot a Hi-C interaction matrix in a square format	plotHicSquare
Plot a Hi-C interaction matrix in a triangular format	plotHicTriangle
Plot a chromosome ideogram with or without cytobands	plotIdeogram
Plot a legend	plotLegend
Plot a Manhattan plot	plotManhattan
Plot multiple signal tracks in line with each other	plotMultiSignal
Plot paired-end genomic range elements	plotPairs
Plot paired-end genomic range data in an arch style	plotPairsArches
Plot a polygon within a plotgardener layout	plotPolygon
Plot genomic range elements in a pileup or collapsed format	plotRanges
Plot a raster object within a plotgardener layout	plotRaster
Plot a rectangle within a plotgardener layout	plotRect
Draw a line segment within a plotgardener layout	plotSegments
Plot any kind of signal track data for a single chromosome	plotSignal
Plot text within a plotgardener layout	plotText
Plot gene transcripts in a pileup style for a single chromosome	plotTranscripts
Read a bigWig file and return it as a data frame	readBigwig
Read a .(m)cool file and return Hi-C data as a dataframe	readCool
Read basepair resolutions from an .(m)cool file	readCoolBpResolutions
Read chromosomes included in .(m)cool files	readCoolChroms
Read normalizations included in .(m)cool files	readCoolNorms
Read a .hic file and return Hi-C data as a dataframe	readHic