plot_browser_tracks {ALPS} | R Documentation |
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.
plot_browser_tracks(data_table, gene_range = NULL, ref_gen = "hg38", cex.axis = 0.5, cex.title = 0.8, ...)
data_table |
a dataframe that contains |
gene_range |
genomic region for which browser-like plots needed in format |
ref_gen |
reference genome, to get gene annotations, currently supports |
cex.axis |
axis label size, default |
cex.title |
axis title size, default |
... |
additional arguments to change the appearence of a plot. All arguments that can be passed to base R graphics are supported |
plot of genome browser tracks
## 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')