plotMsigNetwork {vissE}R Documentation

Plot a gene set overlap network

Description

Plots a network of gene set overlap with overlap computed using the computeMsigOverlap() and a graph created using computeMsigNetwork().

Usage

plotMsigNetwork(
  ig,
  markGroups = NULL,
  genesetStat = NULL,
  nodeSF = 1,
  edgeSF = 1,
  lytFunc = igraph::layout_with_graphopt,
  lytParams = list()
)

Arguments

ig

an igraph object, containing a network of gene set overlaps computed using computeMsigNetwork().

markGroups

a named list, of character vectors or numeric indices specifying node groupings. Each element of the list represent a group and contains a character vector with node names. Up to 12 groups can be visualised in the plot.

genesetStat

a numeric, statistic to project onto the nodes. These could be p-values, log fold-changes or gene set score from a singscore-based analysis.

nodeSF

a numeric, indicating the scaling factor to apply to node sizes.

edgeSF

a numeric, indicating the scaling factor to apply to edge widths.

lytFunc

a function, that computes layouts and returns a matrix with 2 columns specifying the x and y coordinates of nodes. Layout functions in the igraph package can be used here.

lytParams

a named list, containing additional parameters to be passed on to the layout function.

Value

a ggplot2 object

Examples

data(hgsc)
ovlap <- computeMsigOverlap(hgsc)
ig <- computeMsigNetwork(ovlap, hgsc)
groups <- list('g1' = c(1, 9), 'g2' = c(5, 6))

plotMsigNetwork(ig, markGroups = groups)


[Package vissE version 1.0.0 Index]