QCstats.plot: Make plot of ORFik QCreport

In JokingHero/ORFik: Open Reading Frames in Genomics

Make plot of ORFik QCreport

Description

From post-alignment QC relative to annotation, make a plot for all samples. Will contain among others read lengths, reads overlapping leaders, cds, trailers, mRNA / rRNA etc.

Usage

QCstats.plot(stats, output.dir = NULL, plot.ext = ".pdf", as_gg_list = FALSE)

Arguments

stats	the experiment object or path to custom ORFik QC folder where a file called "STATS.csv" is located.
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".
plot.ext	character, default: ".pdf". Alternatives: ".png" or ".jpg".
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.

Value

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

Examples

df <- ORFik.template.experiment()[3,]
## First make QC report
# QCreport(df)
## Now you can get plot
# QCstats.plot(df)

JokingHero/ORFik documentation built on May 3, 2024, 2:34 a.m.