GSEAPlotAtomic: GSEA plot for a single term
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

GSEAPlotAtomic

R Documentation

GSEA plot for a single term

Description

GSEA plot for a single term

Usage

GSEAPlotAtomic(
  data,
  gene_ranks = "@gene_ranks",
  gs,
  genes,
  metric = "p.adjust",
  sample_coregenes = FALSE,
  line_width = 1.5,
  line_alpha = 1,
  line_color = "#6BB82D",
  n_coregenes = 10,
  genes_label = NULL,
  label_fg = "black",
  label_bg = "white",
  label_bg_r = 0.1,
  label_size = 4,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  ...
)

Arguments

`data`	A data frame.
`gene_ranks`	A numeric vector of gene ranks with genes as names The gene ranks are used to plot the gene sets. If `gene_ranks` is a character vector starting with `@`, the gene ranks will be taken from the attribute of `data`.
`gs`	The name of the gene set
`genes`	The genes in the gene set
`metric`	The metric to show in the subtitle
`sample_coregenes`	A logical value to sample the core genes from the core_enrichment; if `FALSE`, the first `n_coregenes` will be used
`line_width`	The width of the line in the running score plot
`line_alpha`	The alpha of the line in the running score plot
`line_color`	The color of the line in the running score plot
`n_coregenes`	The number of core genes to label
`genes_label`	The genes to label. If set, `n_coregenes` will be ignored
`label_fg`	The color of the label text
`label_bg`	The background color of the label
`label_bg_r`	The radius of the background color of the label
`label_size`	The size of the label text
`title`	A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.
`subtitle`	A character string specifying the subtitle of the plot.
`xlab`	A character string specifying the x-axis label.
`ylab`	The label of the y-axis, will be shown on the right side
`...`	Additional arguments.