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)
#> 
#> ── Column specification ────────────────────────────────────────────────────────
#> cols(
#>   sample = col_character(),
#>   `Number of input reads` = col_double(),
#>   `Uniquely mapped reads number` = col_double(),
#>   `Uniquely mapped reads %` = col_character()
#> )

get_star_align_log_summary_plot(x  = file_paths, col_total_reads = "red",
col_mapped_reads = "blue")
#> 
#> ── Column specification ────────────────────────────────────────────────────────
#> cols(
#>   sample = col_character(),
#>   `Number of input reads` = col_double(),
#>   `Uniquely mapped reads number` = col_double(),
#>   `Uniquely mapped reads %` = col_character()
#> )