Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.
Citation
Zuguang Gu, et al., gtrellis: an R/Bioconductor package for making genome-level Trellis graphics, 2016. BMC Bioinformatics.
Install
gtrellis is available on Bioconductor, you can install it by:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("gtrellis") If you want the latest version, install it directly from GitHub:
library(devtools)
install_github("jokergoo/gtrellis")Usage
Basic usage is:
library(gtrellis)
bed = circlize::generateRandomBed()
gtrellis_layout(track_ylim = range(bed[[4]]))
add_track(bed, panel.fun = function(bed) {
x = (bed[[2]] + bed[[3]]) / 2
y = bed[[4]]
grid.points(x, y, pch = 16, size = unit(1, "mm"))
})There are several tracks with pre-defined graphics:
