Plot expression of metabolites in spatially from a Spatial SpaMTP Objects.

This is for plotting values of annotated metabolites stored in a SpaMTP Seurat Object containing an image(i.e. H&E image). This function inherits off Seurat::ImageFeaturePlot(). Look here for more detailed documentation about inputs.

Usage

SpatialMZAnnotationPlot(
  object,
  metabolites,
  plusminus = NULL,
  images = NULL,
  crop = TRUE,
  assay = "Spatial",
  slot = "counts",
  keep.scale = "feature",
  min.cutoff = NA,
  max.cutoff = NA,
  ncol = NULL,
  combine = TRUE,
  pt.size.factor = 1.6,
  alpha = c(1, 1),
  image.alpha = 1,
  stroke = 0.25,
  interactive = FALSE,
  information = NULL,
  column.name = "all_IsomerNames",
  plot.exact = TRUE,
  verbose = TRUE
)

Arguments

object: Seurat Spatial Metabolomic Object to Visualise.
metabolites: Vector of metabolite names to plot (e.g. c("Glucose", "Glutamine")). The Seurat Object provided must contain annotations in the respective assay metadata.
plusminus: Numeric value defining the range/threshold either side of the target peak/peaks to be binned together for plotting (default = NULL).
images: Character string of the name of the image to plot (default = NULL).
crop: Boolean value indicating if to crop the plot to focus on only points being plotted (default = TRUE).
assay: Character string indicating which Seurat object assay to pull data form (default = "Spatial").
slot: Character string indicating the assay slot to use to pull expression values form (default = "counts").
keep.scale: Character string describing how to handle the color scale across multiple plots. Check Seurat::SpatialFeaturePlot() for all options (default = "feature").
min.cutoff: Vector of numeric value describing the minimum cutoff values for each m/z feature (default = NA).
max.cutoff: Vector of numeric value describing the maximum cutoff values for each m/z feature (default = NA).
ncol: Integer defining the number of columns if plotting multiple plots (default = NULL).
combine: Boolean value stating if to combine plots into a single patchworked ggplot object (default = TRUE).
pt.size.factor: Numeric value defining the point size for spots when plotting (default = 1.6).
alpha: Numeric value between 0 and 1 defining the spot alpha (default = 1).
image.alpha: Numeric value between 0 and 1 defining the image alpha (default = 1).
stroke: Numeric value describing the width of the border around the spot (default. =0.25).
interactive: Boolean value of if to launch an interactive SpatialDimPlot or SpatialFeaturePlot session, see Seurat::ISpatialDimPlot() or Seurat::ISpatialFeaturePlot() for more details (default = FALSE).
information: An optional dataframe or matrix of extra infomation to be displayed on hover (default = NULL).
column.name: Character string defining the column name where the annotations are stored in the slot meta.data (default = "all_IsomerNames").
plot.exact: Boolean value describing if to only plot exact matches to the metabolite search terms, else will plot all metabolites which contain serach word in name (default = TRUE).
verbose: Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).

Value

A ggplot showing the Spatial representation of expression data of specified m/z values for Spatial data with H&E Image

Examples

# SpatialMZAnnotationPlot(SeuratObj, mzs = c("Glucose", "Glutamine"))
# SpatialMZAnnotationPlot(SeuratObj, mzs = c("Glucose", "Glutamine"), plusminus = 0.05)