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