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

This function has been adapted from fgsea package. For more detail about function inputs please visit their documentation.

Usage

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

Arguments

pathways

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 dimensionality reduction to use 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 score of each pathway across the relative reduction.

Examples

#PlotPathways(c("Glycolysis", "Acylcarnitine 3-Butenylcarnitine", "ABC transporters"), spamtp_obj, reduction = "umap"))