plotCoregulationProfileSpatial: Plot a spatial expression profile of a gene set

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

Plot a spatial expression profile of a gene set

Description

Plot a spatial expression profile of a gene set

Usage

plotCoregulationProfileSpatial(
  pathway,
  object,
  title = NULL,
  assay = DefaultAssay(object),
  colors = rdbuColors,
  guide = "colourbar",
  image.alpha = 0,
  minLimit = -3,
  maxLimit = 3,
  ...
)

Arguments

pathway	Gene set to plot or a list of gene sets (see details below)
object	Seurat object
title	plot title
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
image.alpha	adjust the opacity of the background images
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.
...	optional arguments for SpatialFeaturePlot

Value

ggplot object (or a list of objects) with the coregulation profile plot

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.