plotTopZ: visualize the top genes contributing to the LVs

View source: R/Allfuncs.R

plotTopZR Documentation

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.