GSEA Summary Plot — GSEASummaryPlot • ggforge

Creates a summary visualization of GSEA (Gene Set Enrichment Analysis) results, showing normalized enrichment scores (NES) with integrated line plots for each term.

Usage

GSEASummaryPlot(
  data,
  in_form = c("auto", "dose", "fgsea"),
  gene_ranks = "@gene_ranks",
  gene_sets = "@gene_sets",
  top_term = 10,
  metric = "p.adjust",
  cutoff = 0.05,
  character_width = 50,
  line_plot_size = 0.25,
  metric_name = metric,
  nonsig_name = "Insignificant",
  linewidth = 0.2,
  line_by = c("prerank", "running_score"),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  alpha = 0.6,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme = "theme_ggforge",
  theme_args = list(),
  palette = "Spectral",
  palcolor = NULL,
  seed = 8525,
  ...
)

Arguments

data

A data frame of GSEA results For example, from DOSE::gseDO() or fgsea::fgsea(). Required columns are ID, Description, NES, p.adjust, pvalue. The ID column is used to match the gene sets.

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.

top_term

An integer to select the top terms

metric

The metric to use for the significance of the terms Typically the column name of p values or adjusted p values. It is also used to select the top terms.

cutoff

The cutoff for the significance of the terms The terms will not be filtered with this cutoff; they are only filtered by the top_term ranked by the metric. The cutoff here is used to show the significance of the terms on the plot. For the terms that are not significant, the color will be grey.

character_width

The width of the characters in the y-axis

line_plot_size

The size of the line plots

metric_name

The name of the metric to show in the color bar

nonsig_name

The name of the legend for the nonsignificant terms

linewidth

The width of the lines in the line plots

line_by

The method to calculate the line plots.

prerank: Use the gene ranks as heights to plot the line plots.
running_score: Use the running score to plot the line plots.

title

Plot title

subtitle

Plot subtitle

xlab

X-axis label

ylab

Y-axis label

alpha

Transparency level (0-1)

aspect.ratio

Aspect ratio of plot panel

legend.position

Legend position: "none", "left", "right", "bottom", "top"

legend.direction

Legend direction: "horizontal" or "vertical"

theme

Theme name (string) or theme function

theme_args

List of arguments passed to theme function

palette

Color palette name

palcolor

Custom colors for palette

seed

Random seed for reproducibility

...

Additional arguments passed to atomic plotting functions.

Value

A ggplot object with height and width attributes

Examples

# \donttest{
data(gsea_example)

# Basic usage
GSEASummaryPlot(gsea_example)


# Use running score instead of prerank
GSEASummaryPlot(gsea_example, line_by = "running_score")


# Adjust significance cutoff
GSEASummaryPlot(gsea_example, cutoff = 0.01)


# Show more terms
GSEASummaryPlot(gsea_example, top_term = 15)


# Customize color palette
GSEASummaryPlot(gsea_example, palette = "RdYlBu")


# Adjust character width for long pathway names
GSEASummaryPlot(gsea_example, character_width = 70)

# }