plot_pileup: Plot pileup profiles

In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

Plot pileup profiles

Description

plot_pileup plots read counts of pileup coverage at base resolution.

Usage

plot_pileup(
  Pileup,
  Ranges,
  cases = NULL,
  logcount = NULL,
  plot.meanpileup = TRUE,
  col.pileup = NULL,
  col.meanpileup = "grey",
  main = NULL,
  cex.main = 1.2,
  print.ranges = TRUE,
  xlim = NULL,
  ylim = NULL,
  xlab = NULL,
  ylab = NULL,
  ...
)

Arguments

Pileup	a pileup object with rows for genomic positions and columns for samples
Ranges	a list of information for genomic regions. get_Ranges.
cases	a vector specifying which samples are to be plotted. Sample IDs matching with the caseIDs in read_BAM or read_pileup can be used. Also, the column numbers can be simply used. e.g. cases=c(1,4,100) will plot the 1st, 4th, 100th columns (i.e. samples) in the Pileup. If NULL, all samples with plotted. Default is NULL.
logcount	a numeric value indicating the number used in the logarithmic transformation. When your data is the log-transformed one, this parameter will print the raw read counts in y-axis labels instead of the log-scale. For example, if your data is Pileup = log10(read depth+c)-log10(c), "c" is the log count. Default is NULL, and y-axis will print labels based on the scale of the Pileup. If your data is not log-scale, use NULL.
plot.meanpileup	a logical value indicating whether the mean coverage should be drawn. Default is TRUE.
col.pileup	colors for the pileup samples
col.meanpileup	a color for the mean coverage. Defult is "darkgrey"
print.ranges	a logical value indicating whether genomic ranges and locus ranges (get_Ranges) should be printed in x-axis.
...	other graphical parameters passed to points.

Examples

## Not run: 
plot_pileup(Pileup=ScissorOutput$logData,Ranges=Ranges,cases=2,logcount=10)

## End(Not run)

hyochoi/SCISSOR documentation built on July 6, 2022, 6:59 a.m.