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",
  database = NULL,
  database_version = "latest",
  database_source = c("auto", "bundled", "local"),
  database_local_dir = NULL,
  ...
)

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").
database: Optional named list of database resources, normally created by LoadSpaMTPDatabase().
database_version: Database snapshot version used for pathway lookup.
database_source: Database source; see LoadSpaMTPDatabase().
database_local_dir: Optional local RDS resource directory.
...: 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

utils::str(formals(PlotPathways))
#> Dotted pair list of 13
#>  $ pathways          : symbol 
#>  $ object            : symbol 
#>  $ title             : NULL
#>  $ assay             : language DefaultAssay(object)
#>  $ slot              : chr "scale.data"
#>  $ reduction         : NULL
#>  $ colors            : language c("darkblue", "lightgrey", "darkred")
#>  $ guide             : chr "colourbar"
#>  $ database          : NULL
#>  $ database_version  : chr "latest"
#>  $ database_source   : language c("auto", "bundled", "local")
#>  $ database_local_dir: NULL
#>  $ ...               : symbol 
#PlotPathways(c("Glycolysis", "Acylcarnitine 3-Butenylcarnitine", "ABC transporters"), spamtp_obj, reduction = "umap"))