get_star_align_log_summary_plot: Visualise alignment stats in a bar plot

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Visualise alignment stats in a bar plot

Description

Visualise alignment stats in a bar plot

Usage

get_star_align_log_summary_plot(
  x,
  is_paired_data = TRUE,
  col_total_reads = "#007e2f",
  col_mapped_reads = "#ffcd12"
)

Arguments

x	a named character vector denoting paths to *Log.final.out file generated by STAR aligner. Names will be used to label Y axis in the plot. If not named, file names will be used to label.
is_paired_data	a logical, default TRUE, denoting whether data is paired or single end. By default STAR counts a paired-end read as one read. When is_paired_data set to TRUE it doubles the count of total and mapped reads.
col_total_reads	a character string denoting bar color total reads. Default "#007e2f".
col_mapped_reads	a character string denoting bar color total reads. Default "#ffcd12".

Value

a bar plot.

Examples

file_dir <- system.file("extdata",package = "parcutils")

file_paths <- fs::dir_ls(path = file_dir,
glob = "*Log.final.out" , recurse = TRUE, type = "file") %>% as.character()

get_star_align_log_summary_plot(x  = file_paths)
get_star_align_log_summary_plot(x  = file_paths, col_total_reads = "red",
col_mapped_reads = "blue")

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.