plotWcorsClusterPathway: plotWcorsClusterPathway

Description Usage Arguments Value

Description

the plotWcorsClusterPathway function plots network graphs with most represented pathways labelled

Usage

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plotWcorsClusterPathway(sigWcorsList, pathways = hallmarks,
  geneUniverse = NULL, cutk = 15, topPathways = 2, cluster = FALSE,
  label_wrap_cut = 20)

Arguments

sigWcorsList

named list of weighted correlation matrices per branch, rows are gene pairs and columns are ordered samples, if it is not a list it will be converted into a list

pathways

is a named list containing gene sets for querying, if left NULL defaults to REACTOME c2.all.v6.1.symbols.gmt downloaded from MSigDB

geneUniverse

is the universe of genes measured, if null its taken as all the genes in the sigWcorsList

cutk

number of weighted correlation clusters to cut hclust

topPathways

is the top number of pathways to plot

cluster

is a logical if pathway and weighted correlation clustering should be performed

label_wrap_cut

number of letters to wrap for labelling heatmap

Value

plot plots of igraph objects


shazanfar/DCARS documentation built on Oct. 14, 2020, 11:11 a.m.