SpatialDimPlot_scCustom: SpatialDimPlot with modified default settings

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

SpatialDimPlot with modified default settings

Description

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

Usage

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

## Not run: 
SpatialDimPlot_scCustom(seurat_object = seurat_object)

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.