codon_usage_plot: Plot codon_usage

In Roleren/ORFik: Open Reading Frames in Genomics

Plot codon_usage

Description

Plot codon_usage

Usage

codon_usage_plot(
  res,
  score_column = res$relative_to_max_score,
  ylab = "Ribo-seq library",
  legend.position = "none",
  limit = c(0, max(score_column)),
  midpoint = max(limit/2),
  monospace_font = TRUE,
  ignore_start_stop_codons = FALSE
)

Arguments

res	a data.table of output from a codon_usage function
score_column	numeric, default: res$relative_to_max_score. Which parameter to use as score column.
ylab	character vector, names for libraries to show on Y axis
legend.position	character, default "none", do not display legend.
limit	numeric, 2 values for plot color limits. Default: c(0, max(score_column))
midpoint	numeric, default: max(limit / 2). midpoint of color limit.
monospace_font	logical, default TRUE. Use monospace font, this does not work on systems (require specific font packages), set to FALSE if it crashes for you.
ignore_start_stop_codons	logical, default FALSE. If TRUE, remove start (#) and stop (*) codons.

Value

a ggplot object

See Also

Other codon: codon_usage(), codon_usage_exp()

Examples

df <- ORFik.template.experiment()[9:10,] # Subset to 2 Ribo-seq libs
## For multiple libs
res2 <- codon_usage_exp(df, outputLibs(df, type = "pshifted", output.mode = "list"),
                 min_counts_cds_filter = 10)
# codon_usage_plot(res2, monospace_font = TRUE) # This gives check error
codon_usage_plot(res2, monospace_font = FALSE) # monospace font looks better

Roleren/ORFik documentation built on April 12, 2025, 5:31 a.m.