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

In fgsea: Fast Gene Set Enrichment Analysis

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)

Example output

Loading required package: Rcpp

fgsea documentation built on Nov. 8, 2020, 5:22 p.m.