This is for plotting SM data from a SpaMTP Seurat Object that does not contain an image(i.e. H&E image). This function inherits from Seurat::ImageFeaturePlot().
Usage
ImageMZPlot(
object,
mzs,
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",
plot.pixel = FALSE,
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).
- 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 image 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").
- 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).