ImageDimPlot: 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
)

Value

If combine = TRUE, a patchwork

ggplot object; otherwise, a list of ggplot objects

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.