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GSEA Plot

Source: R/gsea.R
GSEAPlot.Rd

Creates detailed GSEA plots for one or more gene sets, showing the running enrichment score, gene positions, and ranked list metric for each set.

Usage

GSEAPlot(
  data,
  in_form = c("auto", "dose", "fgsea"),
  gene_ranks = "@gene_ranks",
  gene_sets = "@gene_sets",
  gs = NULL,
  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,
  base_size = 12,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  seed = 8525,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  theme = "theme_ggforge",
  ...
)

Arguments

data

A data frame containing the data to plot

in_form

The format of the input data

  • fgsea: The input data is from the fgsea package.

  • dose: The input data is from the DOSE package.

  • auto: Automatically detect the format of the input data. When "leadingEdge" is in the input data, it will be treated as "fgsea"; otherwise, if "core_enrichment" is in the input data, it will be treated as "dose".

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.

gene_sets

A list of gene sets, typically from a record of a GMT file The names of the list should match the ID column of data. If gene_sets is a character vector starting with @, the gene sets will be taken from the attribute of data. The GSEA plots will be plotted for each gene set. So, the number of plots will be the number of gene sets. If you only want to plot a subset of gene sets, you can subset the gene_sets before passing it to this function.

gs

The names of the gene sets to plot If NULL, all gene sets in gene_sets will be plotted.

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

Plot title

subtitle

Plot subtitle

xlab

X-axis label

ylab

Y-axis label

base_size

Base font size for the plot.

combine

Whether to combine split plots into one

nrow

Number of rows when combining plots

ncol

Number of columns when combining plots

byrow

Fill combined plots by row

seed

Random seed for reproducibility

axes

How to handle axes in combined plots ("keep", "collect", "collect_x", "collect_y")

axis_titles

How to handle axis titles in combined plots

guides

How to handle guides in combined plots ("collect", "keep", "auto")

design

Custom layout design for combined plots

theme

Theme name (string) or theme function

...

Additional arguments passed to atomic plotting functions.

Value

A ggplot object (if single plot) or combined plot object

Examples

# \donttest{
data(gsea_example)

# Plot single gene set
GSEAPlot(gsea_example, gene_sets = attr(gsea_example, "gene_sets")[1])


# Plot multiple gene sets
GSEAPlot(gsea_example, gene_sets = attr(gsea_example, "gene_sets")[1:4])


# Label core genes
GSEAPlot(
  gsea_example,
  gene_sets = attr(gsea_example, "gene_sets")[1],
  n_coregenes = 5
)


# Customize line appearance
GSEAPlot(
  gsea_example,
  gene_sets = attr(gsea_example, "gene_sets")[1],
  line_width = 2,
  line_color = "#FF6B6B"
)


# Return separate plots instead of combined
plots <- GSEAPlot(
  gsea_example,
  gene_sets = attr(gsea_example, "gene_sets")[1:3],
  combine = FALSE
)
# }