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. 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 1.16.0 Index]