RiboQC.plot {ORFik} | R Documentation |
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
RiboQC.plot( df, output.dir = file.path(dirname(df$filepath[1]), "QC_STATS/"), width = 6.6, height = 4.5, plot.ext = ".pdf", type = "pshifted", weight = "score", bar.position = "dodge", BPPARAM = BiocParallel::SerialParam(progressbar = TRUE) )
df |
an ORFik |
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). |
BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
ggplot object as a grid
df <- ORFik.template.experiment() df <- df[3,] #lets only p-shift RFP sample at index 3 #shiftFootprintsByExperiment(df) #RiboQC.plot(df)