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

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

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),
  pathwayLabelStyle = NULL,
  headerLabelStyle = NULL,
  valueStyle = NULL,
  axisLabelStyle = NULL,
  render = NULL
)

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.
pathwayLabelStyle	list with style parameter adjustments for pathway labels. For example, 'list(size=10, color="red")' set the font size to 10 and color to red. See 'cowplot::draw_text' for possible options.
headerLabelStyle	similar to 'pathwayLabelStyle' but for the table header.
valueStyle	similar to 'pathwayLabelStyle' but for NES and p-value columns.
axisLabelStyle	list with style parameter adjustments for stats axis labels. See 'ggplot2::element_text' for possible options.
render	(deprecated)

Value

ggplot object with enrichment barcode plots

Examples

data(examplePathways)
data(exampleRanks)
fgseaRes <- fgsea(examplePathways, exampleRanks, minSize=15, maxSize=500)
topPathways <- fgseaRes[head(order(pval), n=15)][order(NES), pathway]
plotGseaTable(examplePathways[topPathways], exampleRanks,
              fgseaRes, gseaParam=0.5)

ctlab/fgsea documentation built on May 3, 2024, 3:43 p.m.