plotU: plot the U matrix from a PLIER decomposition

In wgmao/PLIER: Pathway-Level Information Extractor (PLIER): a generative model for gene expression data

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 Sept. 1, 2024, 10:25 p.m.