plot_browser_tracks: UCSC Genome browser like plots

In itsvenu/ALPS: AnaLysis routines for ePigenomicS data

Description

Function to plot genome browser like plots given a very minimal information such as a set of bigwig files and a genomics region. Tracks are arranged as they are in given input data.frame. Function uses highly customizable Gviz R/bioconductor package to plot browser like plots.

Usage

plot_browser_tracks(data_table, gene_range = NULL, ref_gen = "hg38",
  cex.axis = 0.5, cex.title = 0.8, ...)

Arguments

data_table	a dataframe that contains bw_path, sample_id and color_code. Tracks are colored according to color_code. Default NULL
gene_range	genomic region for which browser-like plots needed in format chr:start-end. Default NULL
ref_gen	reference genome, to get gene annotations, currently supports hg19 and hg38. Default, hg38
cex.axis	axis label size, default 0.5
cex.title	axis title size, default 0.8
...	additional arguments to change the appearence of a plot. All arguments that can be passed to base R graphics are supported

Value

plot of genome browser tracks

Examples

## load example data

chr21_data_table <- system.file('extdata/bw', 'ALPS_example_datatable.txt', package = 'ALPS', mustWork = TRUE)

## attach path to bw_path and bed_path
d_path <- dirname(chr21_data_table)

chr21_data_table <- read.delim(chr21_data_table, header = TRUE)
chr21_data_table$bw_path <- paste0(d_path, '/', chr21_data_table$bw_path)
chr21_data_table$bed_path <- paste0(d_path, '/', chr21_data_table$bed_path)

gene_range = 'chr21:45643725-45942454'

plot_browser_tracks(data_table = chr21_data_table,
gene_range = gene_range, ref_gen = 'hg38')

itsvenu/ALPS documentation built on Nov. 4, 2019, 2:13 p.m.