ImageDimPlot: Spatial Cluster Plots

In satijalab/seurat: Tools for Single Cell Genomics

Spatial Cluster Plots

Description

Visualize clusters or other categorical groupings in a spatial context

Usage

ImageDimPlot(
  object,
  fov = NULL,
  boundaries = NULL,
  group.by = NULL,
  split.by = NULL,
  cols = NULL,
  shuffle.cols = FALSE,
  size = 0.5,
  molecules = NULL,
  mols.size = 0.1,
  mols.cols = NULL,
  mols.alpha = 1,
  nmols = 1000,
  alpha = 1,
  border.color = "white",
  border.size = NULL,
  na.value = "grey50",
  dark.background = TRUE,
  crop = FALSE,
  cells = NULL,
  overlap = FALSE,
  axes = FALSE,
  combine = TRUE,
  coord.fixed = TRUE,
  flip_xy = TRUE
)

Arguments

object	A Seurat object
fov	Name of FOV to plot
boundaries	A vector of segmentation boundaries per image to plot; can be a character vector, a named character vector, or a named list. Names should be the names of FOVs and values should be the names of segmentation boundaries
group.by	Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class
split.by	A factor in object metadata to split the plot by, pass 'ident' to split by cell identity'
cols	Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by brewer.pal.info. By default, ggplot2 assigns colors. We also include a number of palettes from the pals package. See DiscretePalette for details.
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 vector of molecules to plot
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
nmols	Max number of each molecule specified in 'molecules' to plot
alpha	Alpha value for plotting (default is 1)
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 points when using custom scale
dark.background	Set plot background to black
crop	Crop the plots to area with cells only
cells	Vector of cells to plot (default is all cells)
overlap	Overlay boundaries from a single image to create a single plot; if TRUE, then boundaries are stacked in the order they're given (first is lowest)
axes	Keep axes and panel background
combine	Combine plots into a single patchwork ggplot object.If FALSE, return a list of ggplot objects
coord.fixed	Plot cartesian coordinates with fixed aspect ratio
flip_xy	Flag to flip X and Y axes. Default is FALSE.

Value

If combine = TRUE, a patchwork ggplot object; otherwise, a list of ggplot objects

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.