plotGesecaTable: Plots table of gene set profiles.

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

Plots table of gene set profiles.

Description

Plots table of gene set profiles.

Usage

plotGesecaTable(
  gesecaRes,
  pathways,
  E,
  center = TRUE,
  scale = FALSE,
  colwidths = c(5, 3, 0.8, 1.2, 1.2),
  titles = colnames(E),
  colors = c("blue", "white", "red"),
  pathwayLabelStyle = NULL,
  headerLabelStyle = NULL,
  valueStyle = NULL,
  axisLabelStyle = NULL,
  axisLabelHeightScale = NULL
)

Arguments

gesecaRes	Table with geseca results.
pathways	Pathways to plot table, as in 'geseca' function.
E	gene expression matrix, as in 'geseca' function.
center	a logical value indicating whether the gene expression should be centered to have zero mean before the analysis takes place. The default is TRUE. The value is passed to scale.
scale	a logical value indicating whether the gene expression should be scaled to have unit variance before the analysis takes place. The default is FALSE. The value is passed to scale.
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.
titles	sample titles to use an axis labels. Default to 'colnames(E)'
colors	vector of three colors to use in the color scheme
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 pctVar and p-value columns.
axisLabelStyle	list with style parameter adjustments for sample labels. See 'ggplot2::element_text' for possible options.
axisLabelHeightScale	height of the row with axis labels compared to other rows. When set to 'NULL' the value is determined automatically.

Value

ggplot object with gene set profile plots

ctlab/fgsea documentation built on Dec. 21, 2024, 1:55 p.m.