DimPlot with modified default settings

Creates DimPlot with some of the settings modified from their Seurat defaults (colors_use, shuffle, label).

DimPlot_scCustom(
  seurat_object,
  colors_use = NULL,
  pt.size = NULL,
  reduction = NULL,
  group.by = NULL,
  split.by = NULL,
  split_seurat = FALSE,
  figure_plot = FALSE,
  aspect_ratio = NULL,
  shuffle = TRUE,
  seed = 1,
  label = NULL,
  label.size = 4,
  label.color = "black",
  label.box = FALSE,
  dims = c(1, 2),
  repel = FALSE,
  raster = NULL,
  raster.dpi = c(512, 512),
  num_columns = NULL,
  ggplot_default_colors = FALSE,
  color_seed = 123,
  ...
)

Arguments

seurat_object

Seurat object name.

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.

pt.size

Adjust point size for plotting.

reduction

Dimensionality Reduction to use (if NULL then defaults to Object default).

group.by

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.

split.by

Feature to split plots by (i.e. "orig.ident").

split_seurat

logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.

figure_plot

logical. Whether to remove the axes and plot with legend on left of plot denoting axes labels. (Default is FALSE). Requires split_seurat = TRUE.

aspect_ratio

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

shuffle

logical. Whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. (Default is TRUE).

seed

Sets the seed if randomly shuffling the order of points.

label

Whether to label the clusters. By default if group.by = NULL label = TRUE, and otherwise it is FALSE.

label.size

Sets size of 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).

dims

Which dimensions to plot. Defaults to c(1,2) if not specified.

repel

Repel labels.

raster

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

raster.dpi

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

num_columns

Number of columns in plot layout. Only valid if split.by != NULL.

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). figure_plot parameter/code modified from code by Tim Stuart via twitter: https://twitter.com/timoast/status/1526237116035891200?s=20&t=foJOF81aPSjr1t7pk1cUPg.

Examples

library(Seurat)
DimPlot_scCustom(seurat_object = pbmc_small)