SpatialDimPlot with modified default settings — SpatialDimPlot

Creates SpatialDimPlot with some of the settings modified from their Seurat defaults (colors_use).

SpatialDimPlot_scCustom(
  seurat_object,
  group.by = NULL,
  images = NULL,
  colors_use = NULL,
  crop = TRUE,
  label = FALSE,
  label.size = 7,
  label.color = "white",
  label.box = TRUE,
  repel = FALSE,
  ncol = NULL,
  pt.size.factor = 1.6,
  alpha = c(1, 1),
  image.alpha = 1,
  stroke = 0.25,
  interactive = FALSE,
  combine = TRUE,
  ggplot_default_colors = FALSE,
  color_seed = 123,
  ...
)

Arguments

seurat_object: Seurat object name.
group.by: Name of meta.data column to group the data by
images: Name of the images to use in the plot(s)
colors_use: color palette to use for plotting. By default if number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.
crop: Crop the plot in to focus on points plotted. Set to FALSE to show entire background image.
label: Whether to label the clusters
label.size: Sets the size of the labels
label.color: Sets the color of the label text
label.box: Whether to put a box around the label text (geom_text vs geom_label)
repel: Repels the labels to prevent overlap
ncol: Number of columns if plotting multiple plots
pt.size.factor: Scale the size of the spots.
alpha: Controls opacity of spots. Provide as a vector specifying the min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single alpha value for each plot.
image.alpha: Adjust the opacity of the background images. Set to 0 to remove.
stroke: Control the width of the border around the spots
interactive: Launch an interactive SpatialDimPlot or SpatialFeaturePlot session, see ISpatialDimPlot or ISpatialFeaturePlot for more details
combine: Combine plots into a single gg object; note that if TRUE; themeing will not work when plotting multiple features/groupings
ggplot_default_colors: logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
color_seed: random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.
...: Extra parameters passed to DimPlot.

Value

A ggplot object

References

Many of the param names and descriptions are from Seurat to facilitate ease of use as this is simply a wrapper to alter some of the default parameters https://github.com/satijalab/seurat/blob/master/R/visualization.R (License: GPL-3).

Examples

if (FALSE) {
SpatialDimPlot_scCustom(seurat_object = seurat_object)
}