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,
  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 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).
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.

Value

A ggplot object visualizing the pathway score spatially.

Details

Pathways without matching features in the selected assay slot, or without finite z-scores, produce a warning and a labelled placeholder panel. Their positions in the returned list are preserved. Unknown pathway names produce an error.

Examples

utils::str(formals(PlotPathwaysSpatially))
#> Dotted pair list of 25
#>  $ pathways          : symbol 
#>  $ object            : symbol 
#>  $ images            : symbol 
#>  $ title             : NULL
#>  $ image.alpha       : num 1
#>  $ assay             : language SeuratObject::DefaultAssay(object)
#>  $ slot              : chr "scale.data"
#>  $ colors            : language c("darkblue", "lightgrey", "darkred")
#>  $ guide             : chr "colourbar"
#>  $ crop              : logi TRUE
#>  $ min.cutoff        : logi NA
#>  $ max.cutoff        : logi NA
#>  $ ncol              : NULL
#>  $ pt.size.factor    : num 1.6
#>  $ alpha             : language c(1, 1)
#>  $ image.scale       : chr "lowres"
#>  $ shape             : num 21
#>  $ stroke            : logi NA
#>  $ interactive       : logi FALSE
#>  $ information       : NULL
#>  $ image.labels      : NULL
#>  $ database          : NULL
#>  $ database_version  : chr "latest"
#>  $ database_source   : language c("auto", "bundled", "local")
#>  $ database_local_dir: NULL
#PlotPathwaysSpatially(c("Glycolysis", "Acylcarnitine 3-Butenylcarnitine", "ABC transporters"), spamtp_obj)