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 = c("darkblue", "lightgrey", "darkred"),
  guide = "colourbar",
  image.alpha = 0,
  ...
)

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 three colors to use in the color scheme
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
...	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 Oct. 10, 2024, 10:31 a.m.