plotMsigPPI {vissE} | R Documentation

## 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)

[Package vissE version 1.2.2 Index]