plotMsigPPI {vissE} | R Documentation |
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() )
ppidf |
a data.frame, containing a protein-protein interaction from the
IMEx database. This can be retrieved from the |
msigGsc |
a GeneSetCollection object, containing gene sets from the
MSigDB. The |
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 |
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
|
lytParams |
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) plotMsigPPI(ppi, hgsc, grps)