RiboQC.plot: Quality control for pshifted Ribo-seq data

In JokingHero/ORFik: Open Reading Frames in Genomics

Quality control for pshifted Ribo-seq data

Description

Combines several statistics from the pshifted reads into a plot:
-1 Coding frame distribution per read length
-2 Alignment statistics
-3 Biotype of non-exonic pshifted reads
-4 mRNA localization of pshifted reads

Usage

RiboQC.plot(
  df,
  output.dir = QCfolder(df),
  width = 6.6,
  height = 4.5,
  plot.ext = ".pdf",
  type = "pshifted",
  weight = "score",
  bar.position = "dodge",
  as_gg_list = FALSE,
  BPPARAM = BiocParallel::SerialParam(progressbar = TRUE)
)

Arguments

df	an ORFik experiment
output.dir	NULL or character path, default: NULL, plot not saved to disc. If defined saves plot to that directory with the name "/STATS_plot.pdf".
width	width of plot, default 6.6 (in inches)
height	height of plot, default 4.5 (in inches)
plot.ext	character, default: ".pdf". Alternatives: ".png" or ".jpg".
type	type of library loaded, default pshifted, warning if not pshifted might crash if too many read lengths!
weight	which column in reads describe duplicates, default "score".
bar.position	character, default "dodge". Should Ribo-seq frames per read length be positioned as "dodge" or "stack" (on top of each other).
as_gg_list	logical, default FALSE. Return as a list of ggplot objects instead of as a grob. Gives you the ability to modify plots more directly.
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.

Value

the plot object, a grob of ggplot objects of the the data

Examples

df <- ORFik.template.experiment()
df <- df[9,] #lets only p-shift RFP sample at index 9
#shiftFootprintsByExperiment(df)
#RiboQC.plot(df, tempdir())

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.