Plots the spatial expression profile of a feature set corresponding to specified pathways

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

Usage

PlotPathwaysSpatially(
  pathways,
  object,
  images,
  title = NULL,
  image.alpha = 1,
  assay = SeuratObject::DefaultAssay(object),
  slot = "scale.data",
  colors = c("darkblue", "lightgrey", "darkred"),
  guide = "colourbar",
  crop = TRUE,
  min.cutoff = NA,
  max.cutoff = NA,
  ncol = NULL,
  pt.size.factor = 1.6,
  alpha = c(1, 1),
  image.scale = "lowres",
  shape = 21,
  stroke = NA,
  interactive = FALSE,
  information = NULL,
  image.labels = 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 spatial data and coordinates for plotting.
images: Character vector specifying which images to use for plotting from the SpaMTP Seurat Object.
title: Optional title for the plot. If set to NULL the title will be the pathway name (default = NULL).
image.alpha: Numeric value between 0 and 1 controlling the transparency of the underlying image (default = 1).
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").
colors: Vector of colors for the gradient (default = c("darkblue", "lightgrey", "darkred")).
guide: Character string stating the type of legend to display (default = "colourbar").
crop: Boolean logical indicating whether to crop images (default = TRUE).
min.cutoff: Numeric value defining the minimum cutoff value for color scale. If NA this value will be determined based on the minimum value of the dataset (default = NA).
max.cutoff: Numeric value defining the maximum cutoff value for color scale. If NA this value will be determined based on the maximum value of the dataset (default = NA).
ncol: Numeric value defining Number of columns for arranging plots. Note this is useful if multiple images have been supplied/containing within the one SpaMTP Seurat Object (default = NULL).
pt.size.factor: Numeric value defining the spot point size for plotting (default = 1.6).
alpha: Numeric vector controlling the transparency of points (default = c(1,1).
image.scale: Character string defining the image resolution to use. This can be either "hires" or "lowres" (default = "lowres").
shape: Integer value defining the shape of points. If shape = 21, circles will be plotted (default = 21).
stroke: Numeric value stating the stroke width for points (default = NA).
interactive: Boolean logical indicating whether to create interactive plots. NOTE: this functionality is implemented through Seurat::SpatialFeaturePlot (default = FALSE).
information: An optional data.frame or matrix of extra information to be displayed on hover. NOTE: this functionality is implemented through Seurat::SpatialFeaturePlot (default = NULL).
image.labels: Character vector specifying optional labels for multiple images (default = NULL).

Value

A ggplot object visualizing the pathway score spatially.

Examples

#PlotPathwaysSpatially(c("Glycolysis", "Acylcarnitine 3-Butenylcarnitine", "ABC transporters"), spamtp_obj)