plotGseaTable {fgsea} | R Documentation

## Plots table of enrichment graphs using ggplot and gridExtra.

### Description

Plots table of enrichment graphs using ggplot and gridExtra.

### Usage

    plotGseaTable(
      pathways,
      stats,
      fgseaRes,
      gseaParam = 1,
      colwidths = c(5, 3, 0.8, 1.2, 1.2),
      render = TRUE
    )

### Arguments

`pathways` | Pathways to plot table, as in 'fgsea' function.
`stats` | Gene-level stats, as in 'fgsea' function.
`fgseaRes` | Table with fgsea results.
`gseaParam` | GSEA-like parameter. Adjusts displayed statistic values, values closer to 0 flatten plots. Default = 1, value of 0.5 is a good choice too.
`colwidths` | Vector of five elements corresponding to column width for grid.arrange. Can be both units and simple numeric vector, in latter case it defines proportions, not actual sizes. If column width is set to zero, the column is not drawn.
`render` | If true, the plot is rendered to the current device. Otherwise, the grob is returned. Default is true.

### Value

TableGrob object returned by grid.arrange.

### Examples

    data(examplePathways)
    data(exampleRanks)
    fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000,
                      minSize=15, maxSize=100)
    topPathways <- fgseaRes[head(order(pval), n=15)][order(NES), pathway]
    ## Not run:
    plotGseaTable(examplePathways[topPathways], exampleRanks,
                  fgseaRes, gseaParam=0.5)

    ## End(Not run)

[Package fgsea version 1.20.0 Index]