plotCoregulationProfileImage: Spatial visualization of GESECA scores for individual cells

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

Spatial visualization of GESECA scores for individual cells

Description

This function computes GESECA scores for one or more gene sets and overlays those scaled scores onto the spatial image.

Usage

plotCoregulationProfileImage(
  pathway,
  object,
  title = NULL,
  assay = DefaultAssay(object),
  colors = rdbuColors,
  guide = "colourbar",
  minLimit = -3,
  maxLimit = 3,
  ...
)

Arguments

pathway	Gene set (vector of gene names) or a named list of gene sets to plot. If a list is provided, each element is treated as a separate pathway and yields its own plot.
object	Seurat object
title	Optional title for the plot. If 'pathway' is a list, 'title' should be a character vector of the same length; otherwise, the list element names are used.
assay	assay to use for obtaining scaled data, preferably with the same universe of genes in the scaled data
colors	vector of colors to use in the color scheme (default is similar to "RdBu" Brewer's color palette)
guide	option for 'ggplot2::scale_color_gradientn' to control for presence of the color legend the same universe of genes in the scaled data
minLimit	Numeric value specifying the minimum limit for the color scale. This defines the lower bound of the z-score used in coloring the feature plot. Values below this limit are squished to the minimum color.
maxLimit	Numeric value specifying the maximum limit for the color scale. This defines the upper bound of the z-score used in coloring the feature plot. Values above this limit are squished to the maximum color.
...	Additional arguments passed to ImageFeaturePlot

Value

ggplot object (or a list of objects) with the spatial image plot of scaled geseca scores

When the input is a list of pathways, pathway names are used for titles. A list of ggplot objects a returned in that case.

ctlab/fgsea documentation built on June 11, 2025, 5:16 p.m.