Plot expression of m/z values spatially for a Spatial SpaMTP Seurat Objects.
Source:R/PlottingSpaMTP.R
SpatialMZPlot.RdThis is for plotting SM m/z data from a SpaMTP Seurat Object that contains an image (i.e. H&E image). This function inherits off Seurat::SpatialFeaturePlot(). Look here for more detailed documentation about inputs.
Usage
SpatialMZPlot(
object,
mzs,
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,
verbose = TRUE
)Arguments
- object
Seurat Spatial Metabolomic Object to Visualise.
- mzs
Vector of numeric m/z values to plot (e.g. c(400.1578, 300.1)). The function FindNearestMZ() is used to automatically find the nearest m/z value to the ones given.
- 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 information to be displayed on hover (default = NULL).
- verbose
Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).