plotMsigNetwork {vissE} | R Documentation

## Plot a gene set overlap network

### Description

Plots a network of gene set overlap with overlap computed using the `computeMsigOverlap()` and a graph created using `computeMsigNetwork()`.

### Usage

    plotMsigNetwork(
      ig,
      markGroups = NULL,
      genesetStat = NULL,
      nodeSF = 1,
      edgeSF = 1,
      lytFunc = "graphopt",
      lytParams = list()
    )

### Arguments

`ig` | an igraph object, containing a network of gene set overlaps computed using `computeMsigNetwork()`.
`markGroups` | a named list, of character vectors. Each element of the list represent a group and contains a character vector with node names. Up to 12 groups can be visualised in the plot.
`genesetStat` | a named numeric, statistic to project onto the nodes. These could be p-values, log fold-changes or gene set score from a singscore-based analysis.
`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 ggplot2 object

### Examples

    data(hgsc)
    ovlap <- computeMsigOverlap(hgsc, thresh = 0.15)
    ig <- computeMsigNetwork(ovlap, hgsc)
    groups <- list(
      'g1' = c("HALLMARK_HYPOXIA", "HALLMARK_GLYCOLYSIS"),
      'g2' = c("HALLMARK_INTERFERON_GAMMA_RESPONSE")
    )

    plotMsigNetwork(ig, markGroups = groups)

[Package vissE version 1.2.2 Index]