plotCummPAindex: Plot distribution of PA index among biological samples.

In BMILAB/movAPA: movAPA: Modeling and Visualization of Dynamics of Alternative PolyAdenylation

Plot distribution of PA index among biological samples.

Description

PlotCummPAindex plots distribution of PA index among biological samples by calculating the cumulative fraction.

Usage

plotCummPAindex(
  PAindex,
  groupName = "Sample",
  xlab,
  ylab = "Cumulative fraction"
)

Arguments

PAindex	a matrix of PAindex, which is normally from movAPAindex() or movPAindex().
groupName	shown as the legend title.
xlab	x label.
ylab	y label, default is "Cumulative fraction".

Value

A ggplot2 plot object.

See Also

Other comparison functions: movAPAindexDiff(), movAPAindex(), movAPAswitch(), movDEGene(), movDEPAC(), movPAindex(), movUTRtrend()

Examples

data(scPACds)
scPACdsCt=subsetPACds(scPACds, group='celltype', pool=TRUE)
scPACdsCt=get3UTRAPAds(scPACdsCt, sortPA=TRUE, choose2PA='PD')
## Cummlative plot of GPI index.
gpi=movAPAindex(scPACdsCt, method="GPI")
plotCummPAindex(PAindex=gpi, groupName='cell type', xlab='GPI')
## The plot of the distribution of Shannon index (tissue-specificity) for each PAC.
shan=movPAindex(scPACdsCt, method="shan")
plotCummPAindex(PAindex=shan[, -c(1:3)], groupName='cell type', xlab='Shannon index')

BMILAB/movAPA documentation built on Jan. 3, 2024, 11:09 p.m.