plotTopZallPath: visualize the top genes contributing to the LVs similarily to...

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

visualize the top genes contributing to the LVs similarily to plotTopZ. However in this case all the pathways contributing to each LV are show seperatly. Useful for seeing pathway usage for a single LV or understading the differences between two closely related LVs

Description

visualize the top genes contributing to the LVs similarily to plotTopZ. However in this case all the pathways contributing to each LV are show seperatly. Useful for seeing pathway usage for a single LV or understading the differences between two closely related LVs

Usage

plotTopZallPath(
  plierRes,
  data,
  priorMat,
  top = 10,
  index = NULL,
  regress = F,
  fdr.cutoff = 0.2,
  ...
)

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 genes.
fdr.cutoff	Significance cutoff for a pathway to be plotted
...	Additional arguments to be passed to pheatmap, such as a column annotation data.frame

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