ggbio — Bioconductor データを ggplot2 的に描画

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

source("https://bioconductor.org/biocLite.R")
biocLite('ggbio')
library(ggbio)

使い方

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()