Heavy Watal

ggbio — Bioconductor データを ggplot2 的に描画

http://www.tengfei.name/ggbio/

Yin, Cook, and Lawrence (2012) ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biology 13:R77 https://www.ncbi.nlm.nih.gov/pubmed/22937822

Bioconductor を読み込んでインストール

BiocManager::install("ggbio")
library(ggbio)

使い方

http://www.tengfei.name/ggbio/docs/man/

autoplot(gr, ...)
xlab, ylab, main
trancate.gaps=FALSE
truncate.fun=NULL
ratio=0.0025
space.skip=0.1
legend=TRUE
geom=NULL
stat=NULL
coord=c("default", "genome", "truncate_gaps")
layout=c("linear", "karyogram", "circle")

plotSingleChrom(), plotIdeogram(), Ideogram()

plotStackedOverview(), plotKaryogram()

plotGrandLinear()


geom_alignment()

geon_arch()

geom_arrow()

geom_arrowrect()

geom_bar()

geom_chevron()

geom_rect()

geom_segment()


layout_karyogram(data, ...)

layout_circle()


stat_aggregate stat_bin stat_coverage stat_gene stat_identity stat_mismatch stat_reduce stat_slice stat_stepping stat_table


theme_alignment theme_clear theme_genome theme_noexpand theme_null theme_pack_panels theme_tracks_sunset


tracks(...)
複数のトラックをひとつの図にまとめる
heights, xlim,
xlab, main, title, theme,
track.plot.color, track.bg.color,
main.height=unit(1.5, "lines"),
scale.height=unit(1, "lines"),
xlab.height=unit(1.5, "lines"),
padding=unit(-1, "lines"),
label.bg.color="white", label.bg.fill="gray80",
label.text.color="black", label.text.cex=1,
label.width=unit(2.5, "lines")

zoom(), zoom_in(), zoom_out()

nextView() , prevView()

biovizBase

https://master.bioconductor.org/packages/release/bioc/html/biovizBase.html