R: Plots table of enrichment graphs using ggplot and gridExtra.

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))

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.

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 1.6.0 Index]