plotTopZ: visualize the top genes contributing to the LVs

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

visualize the top genes contributing to the LVs

Description

visualize the top genes contributing to the LVs

Usage

plotTopZ(
  plierRes,
  data,
  priorMat,
  top = 10,
  index = NULL,
  regress = F,
  allLVs = F,
  ...
)

Arguments

plierRes	the result returned by PLIER
data	the data to be displayed in a heatmap, typically the z-scored input data (or some subset thereof)
priorMat	the same gene by geneset binary matrix that was used to run PLIER
top	the top number of genes to use
index	the subset of LVs to display
regress	remove the effect of all other LVs before plotting top genes, will take longer but can be useful to see distinct patterns in highly correlated LVs.
allLVs	plot even the LVs that have no pathway association
...	Additional arguments to be passed to pheatmap, such as a column annotation data.frame (annotation_col). See ?pheatmap for details.

wgmao/PLIER documentation built on Sept. 1, 2024, 10:25 p.m.