plotU: plot the U matrix from a PLIER decomposition

View source: R/Allfuncs.R

plotUR Documentation

plot the U matrix from a PLIER decomposition

Description

plot the U matrix from a PLIER decomposition

Usage

plotU(
  plierRes,
  auc.cutoff = 0.6,
  fdr.cutoff = 0.05,
  indexCol = NULL,
  indexRow = NULL,
  top = 3,
  sort.row = F,
  ...
)

Arguments

plierRes

the result returned by PLIER

auc.cutoff

the AUC cutoff for pathways to be displayed, increase to get a smaller subset of U

fdr.cutoff

the significance cutoff for the pathway-LV association

indexCol

restrict to a subset of the columns (LVs)

indexRow

restrict to a subset of rows (pathways). Useful if only interested in pathways of a specific type

top

the number of top pathways to discplay for each LV

sort.row

do not custer the matrix but instead sort it to display the positive values close do the 'diagonal'

...

options to be passed to pheatmap


wgmao/PLIER documentation built on May 11, 2022, 10:34 p.m.