SingleImagePlot: Single Spatial Plot

In Seurat: Tools for Single Cell Genomics

Single Spatial Plot

Description

Single Spatial Plot

Usage

SingleImagePlot(
  data,
  col.by = NA,
  col.factor = TRUE,
  cols = NULL,
  shuffle.cols = FALSE,
  size = 0.1,
  molecules = NULL,
  mols.size = 0.1,
  mols.cols = NULL,
  mols.alpha = 1,
  alpha = molecules %iff% 0.3 %||% 0.6,
  border.color = "white",
  border.size = NULL,
  na.value = "grey50",
  dark.background = TRUE,
  ...
)

Arguments

data	A data frame with at least the following columns: “x”: Spatial-resolved x coordinates, will be plotted on the y-axis “y”: Spatially-resolved y coordinates, will be plotted on the x-axis “cell”: Cell name “boundary”: Segmentation boundary label; when plotting multiple segmentation layers, the order of boundary transparency is set by factor levels for this column Can pass NA to data suppress segmentation visualization
col.by	Name of column in data to color cell segmentations by; pass NA to suppress coloring
col.factor	Are the colors a factor or discrete?
cols	Colors for cell segmentations; can be one of the following: NULL for default ggplot2 colors A numeric value or name of a color brewer palette Name of a palette for DiscretePalette A vector of colors equal to the length of unique levels of data$col.by
shuffle.cols	Randomly shuffle colors when a palette or vector of colors is provided to cols
size	Point size for cells when plotting centroids
molecules	A data frame with spatially-resolved molecule coordinates; should have the following columns: “x”: Spatial-resolved x coordinates, will be plotted on the y-axis “y”: Spatially-resolved y coordinates, will be plotted on the x-axis “molecule”: Molecule name
mols.size	Point size for molecules
mols.cols	A vector of color for molecules. The "Set1" palette from RColorBrewer is used by default.
mols.alpha	Alpha value for molecules, should be between 0 and 1
alpha	Alpha value, should be between 0 and 1; when plotting multiple boundaries, alpha is equivalent to max alpha
border.color	Color of cell segmentation border; pass NA to suppress borders for segmentation-based plots
border.size	Thickness of cell segmentation borders; pass NA to suppress borders for centroid-based plots
na.value	Color value for NA segmentations when using custom scale
...	Ignored

Value

A ggplot object

Seurat documentation built on Nov. 18, 2023, 1:10 a.m.