Plots the expression profile of a feature set corresponding to specified pathways onto a 2D scatter plot based on a dimensionality reduction technique.

NOTE: This is a helper function for PlotPathways. This function has been adapted from fgsea package. For more detail about function inputs please visit their documentation.

Usage

PlotSinglePathway(
  pathway,
  object,
  title = NULL,
  assay = DefaultAssay(object),
  slot = "scale.data",
  reduction = NULL,
  colors = c("darkblue", "lightgrey", "darkred"),
  guide = "colourbar",
  ...
)

Arguments

pathway: Character vector of pathway names to plot. These pathways must be those stored in the chempathway object. To check call unique(chempathway$pathwayName).
object: SpaMTP Seurat object containing the spatial data and coordinates for plotting.
title: Optional title for the plot. If set to NULL the title will be the pathway name (default = NULL).
assay: Character string defining the name of assay to use for data extraction. This assay should contain RAMP_IDs as feature names (default = SeuratObject::DefaultAssay(object)).
slot: Character string defining the name of slot to extract data from (default = "scale.data").
reduction: Character string defining which dimensionality reduction to use. If not specified, first searches for 'umap', then 'tsne', then 'pca' (default = NULL).
colors: Vector of colors for the gradient (default = c("darkblue", "lightgrey", "darkred")).
guide: Character string stating the type of legend to display (default = "colourbar").
...: Additional inputs taken by Seurat::FeaturePlot(). Check the relative documentation for more infomation.

Value

A ggplot object visualizing the pathway score spatially.

Examples

#glycolysis_list <- list("Glycolysis" = c("RAMP_C_000218730","RAMP_G_000012583","RAMP_G_000001171","RAMP_G_000007564","RAMP_C_000218226","RAMP_C_000040403","RAMP_C_000001115","RAMP_G_000008859"))
#PlotSinglePathway(glycolysis_list, spamtp_obj, reduction = "umap")