Skip to contents

Plot mass intensity spectra

Source: R/PlottingSpaMTP.R
MassIntensityPlot.Rd

This function plots mean mass spectra intensity values for a given SpaMTP Seurat Object, and groups/splits by categories if supplied.

Usage

MassIntensityPlot(
  data,
  group.by = NULL,
  split.by = NULL,
  cols = NULL,
  assay = "Spatial",
  slot = "counts",
  label.annotations = FALSE,
  annotation.column = "all_IsomerNames",
  mz.labels = NULL,
  metabolite.labels = NULL,
  xlab = "m/z",
  ylab = "intensity",
  mass.range = NULL,
  y.lim = NULL,
  labelCex = 5,
  labelAdj = -1,
  labelOffset = 0,
  labelCol = "#eb4034",
  nlabels.to.show = NULL
)

Arguments

data

Seurat object containing data to be plot.

group.by

Character string defining the name of the meta.data column to group the data by. Results from each group will be overlayed on the one plot (default = NULL).

split.by

Character string defining the name of the meta.data column to group and split the data by. Results from each group will be plotted individually (default = NULL).

cols

Vector of character strings defining the colours to be used to identify each group (default = NULL).

assay

Character string defining the relative Seurat Object assay to pull the required intensity data from (default = "Spatial").

slot

Character string defining the relative slot from the Seurat Object assay to pull the required intensity data from (default = "counts").

label.annotations

Boolean value defining whether to plot metabolite annotations of the supplied mz.labels or metabolite.labels on the plot (default = FALSE).

annotation.column

Character string defining the name of the feature meta.data column which contains the stored m/z annotations (default = "all_IsomerNames").

mz.labels

Vector of character strings defining the m/z values to display on the plot (default = NULL).

metabolite.labels

Vector of character strings defining the metabolite names to display on the plot (default = NULL).

xlab

Character string describing the x-axis title (default = "m/z").

ylab

Character string describing the y-axis title (default = "intensity").

mass.range

Vector of numeric values defining the range of m/z values to include (default = NULL).

y.lim

Vector of numeric values defining the range of intensity values to include (default = NULL).

labelCex

Numeric values for character expansion factor. Seen graphics::text() for more details (default = 0.7).

labelAdj

One or two values in [0,1] which specify the x and y adjustments for the label. Seen graphics::text() for more details (default = NULL).

labelOffset

Value that controls the distance of the text label from the specified coordinates. Seen graphics::text() for more details (default = 0).

labelCol

Character string defining the colour of the annotation labels (default = "#eb4034").

nlabels.to.show

Numeric value defining the number of annotations to show per m/z (default = NULL).

Value

A mass spectrometry plot displaying mean intensity values

Examples

## Plot mean of whole tissue section
# MassIntensityPlot(SeuratObj)

## Plot ssc segmentation groups on the same plot
# MassIntensityPlot(SeuratObj, group.by = "ssc")

## Plot mean of each ssc segmentation of separate plot with mz annotations
# MassIntensityPlot(SeuratObj, split.by= "ssc", mz.labels = c(329.166), plot.layout = c(5,2))

## Plot mean of each ssc segmentation of separate plot with metabolite annotations
# MassIntensityPlot(SeuratObj, split.by= "ssc", mz.labels = c(329.166), label.annotations = TRUE)