plotMsigPPI: Plot PPI network for gene-set clusters identified using vissE

In DavisLaboratory/enrichnets: Visualising Set Enrichment Analysis Results

Plot PPI network for gene-set clusters identified using vissE

Description

This function plots the protein-protein interaction (PPI) network for a gene-set cluster identified using vissE. The international molecular exchange (IMEx) PPI is used to obtain PPIs for genes present in a gene-set cluster.

Usage

plotMsigPPI(
  ppidf,
  msigGsc,
  groups,
  geneStat = NULL,
  statName = "Gene-level statistic",
  threshConfidence = 0,
  threshFrequency = 0.25,
  threshStatistic = 0,
  threshUseAbsolute = TRUE,
  topN = 5,
  nodeSF = 1,
  edgeSF = 1,
  lytFunc = "graphopt",
  lytParams = list()
)

Arguments

ppidf	a data.frame, containing a protein-protein interaction from the IMEx database. This can be retrieved from the msigdb::getIMEX() function.
msigGsc	a GeneSetCollection object, containing gene sets from the MSigDB. The GSEABase::getBroadSets() function can be used to parse XML files downloaded from MSigDB.
groups	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.
geneStat	a named numeric, containing the statistic to be displayed. The vector must be named with either gene Symbols or Entrez IDs depending on annotations in msigGsc.
statName	a character, specifying the name of the statistic.
threshConfidence	a numeric, specifying the confidence threshold to apply to determine high confidence interactions. This should be a value between 0 and 1 (default is 0).
threshFrequency	a numeric, specifying the frequency threshold to apply to determine more frequent genes in the gene-set cluster. The frequecy of a gene is computed as the proportion of gene-sets to which the gene belongs. This should be a value between 0 and 1 (default is 0.25).
threshStatistic	a numeric, specifying the threshold to apply to gene-level statistics (e.g. a log fold-change). This should be a value between 0 and 1 (default is 0).
threshUseAbsolute	a logical, indicating whether the threshStatistic threshold should be applied to absolute values (default TRUE). This can be used to threshold on statistics such as the log fold-chage from a differential expression analysis.
topN	a numeric, specifying the number of genes to label. The top genes are those with the largest count and statistic.
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()).

Value

a ggplot object with the protein-protein interaction networks plot for each gene-set cluster.

Examples

data(hgsc)
grps = list('early' = 'HALLMARK_ESTROGEN_RESPONSE_EARLY', 'late' = 'HALLMARK_ESTROGEN_RESPONSE_LATE')
ppi = msigdb::getIMEX(org = 'hs', inferred = TRUE)
plotMsigPPI(ppi, hgsc, grps)

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