plotMsigNetwork: Plot a gene set overlap network

In DavisLaboratory/enrichnets: Visualising Set Enrichment Analysis Results

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 = "graphopt",
  lytParams = list(),
  rmUnmarkedGroups = FALSE,
  maxGrp = 12
)

Arguments

ig	an igraph object, containing a network of gene set overlaps computed using computeMsigNetwork().
markGroups	a named list, of character vectors. 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 named 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 character, specifying the layout to use (see ggraph::create_layout()).
lytParams	a named list, containing additional parameters needed for the layout (see ggraph::create_layout()).
rmUnmarkedGroups	a logical, indicating whether unmarked groups should be removed from the network (TRUE) or retained (FALSE - default).
maxGrp	a numeric, specifying the maximum number of groups to plot.

Value

a ggplot2 object

Examples

data(hgsc)
ovlap <- computeMsigOverlap(hgsc, thresh = 0.15)
ig <- computeMsigNetwork(ovlap, hgsc)
groups <- list(
  'g1' = c("HALLMARK_HYPOXIA", "HALLMARK_GLYCOLYSIS"),
  'g2' = c("HALLMARK_INTERFERON_GAMMA_RESPONSE")
)

plotMsigNetwork(ig, markGroups = groups)

DavisLaboratory/enrichnets documentation built on Feb. 2, 2024, 9:14 a.m.