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() )
a data.frame, containing a protein-protein interaction from the
IMEx database. This can be retrieved from the
a GeneSetCollection object, containing gene sets from the
GSEABase::getBroadSets() function can be used to parse XML
files downloaded from MSigDB.
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.
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.
a character, specifying the name of the statistic.
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).
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).
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).
a logical, indicating whether the
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.
a numeric, specifying the number of genes to label. The top genes are those with the largest count and statistic.
a numeric, indicating the scaling factor to apply to node sizes.
a numeric, indicating the scaling factor to apply to edge widths.
a character, specifying the layout to use (see
a named list, containing additional parameters needed for
the layout (see
a ggplot object with the protein-protein interaction networks plot for each gene-set cluster.
data(hgsc) grps = list('early' = 'HALLMARK_ESTROGEN_RESPONSE_EARLY', 'late' = 'HALLMARK_ESTROGEN_RESPONSE_LATE') ppi = msigdb::getIMEX(org = 'hs', inferred = TRUE) #> snapshotDate(): 2021-10-18 #> 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