Plot PPI network for gene-set clusters identified using vissE

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.

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)
#> snapshotDate(): 2022-10-03
#> see ?msigdb and browseVignettes('msigdb') for documentation
#> loading from cache
plotMsigPPI(ppi, hgsc, grps)
#> Warning: Assuming the organism to be human.
#> Warning: Ignoring unknown parameters: size
#> Warning: Ignoring unknown aesthetics: text