Plot expression of annotated metabolites spatially — ImageMZAnnotationPlot • SpaMTP

This is for plotting annotated SM data from a SpaMTP Seurat Object that does not contain an image(i.e. H&E image). This function inputs the metabolite name such as 'Glutamine' rather then a specific m/z value. For m/z values please use ImageMZPlot().This function inherits off Seurat::ImageFeaturePlot().

Usage

ImageMZAnnotationPlot(
  object,
  metabolites,
  plusminus = NULL,
  fov = NULL,
  boundaries = NULL,
  cols = if (isTRUE(x = blend)) {
     c("lightgrey", "#ff0000", "#00ff00")
 } else {
   
     c("lightgrey", "firebrick1")
 },
  size = 0.5,
  min.cutoff = NA,
  max.cutoff = NA,
  split.by = NULL,
  molecules = NULL,
  mols.size = 0.1,
  mols.cols = NULL,
  nmols = 1000,
  alpha = 1,
  border.color = "white",
  border.size = NULL,
  dark.background = TRUE,
  blend = FALSE,
  blend.threshold = 0.5,
  crop = FALSE,
  cells = NULL,
  scale = c("feature", "all", "none"),
  overlap = FALSE,
  axes = FALSE,
  combine = TRUE,
  coord.fixed = TRUE,
  assay = "Spatial",
  slot = "data",
  column.name = "all_IsomerNames",
  plot.exact = TRUE,
  plot.pixel = FALSE,
  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).
fov: Character string of name of FOV to plot (default = NULL).
boundaries: A vector of segmentation boundaries per image to plot (default = NULL).
cols: Vector of character strings defining colours used for plotting (default = c("lightgrey", "firebrick1")).
size: Numeric value defining the point size for cells/spots when plotting (default = 0.5).
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).
split.by: Character string defining a factor in the Seurat Object metadata to split the feature plot by (default = NULL).
molecules: Vector of character strings describing molecules to plot (default = NULL).
mols.size: Numeric value for the point size of molecules to plot (default = 0.1).
mols.cols: A vector of colours for the molecules to plot (default = NULL).
nmols: Integer of the max number of each molecule specified in 'molecules' to be plot (default = 1000).
alpha: Numeric value between 0 and 1 defining the spot alpha (default = 1).
border.color: Character string specifying the colour of each spot/cell border (default = white).
border.size: Numeric value for the thickness of the cell segmentation border (default = NULL).
dark.background: Boolean value indicating if the plot background is coloured black (default = FALSE).
blend: Boolean value indicating whether to scale and blend expression values to visualize coexpression of two features (default = FALSE).
blend.threshold: Numeric value defining the color cutoff from weak signal to strong signal; ranges from 0 to 1 (default = 0.5).
crop: Boolean value of whether to crop the plots to area with cells only (default = FALSE).
cells: Vector of character strings defining a group of cells to plot (default = NUll; plots all cells).
scale: Set color scaling across multiple plots; c("features", "all", "none").
overlap: Overlay boundaries from a single image to create a single plot (default = FALSE).
axes: Boolean defining if to keep axes and panel background (default = FALSE).
combine: Boolean value stating if to combine plots into a single patchworked ggplot object (default = TRUE).
coord.fixed: Boolean value of it to plot cartesian coordinates with fixed aspect ratio (default = TURE).
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").
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).
plot.pixel: Boolean indicating if the plot should display pixel square shapes, if false will plot with spots (deafult = FALSE).
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 metabolites.

Examples

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