Stacked Violin Plot

Source: R/Seurat_Plotting.R

Code for creating stacked violin plot gene expression.

Stacked_VlnPlot(
  seurat_object,
  features,
  group.by = NULL,
  split.by = NULL,
  idents = NULL,
  x_lab_rotate = FALSE,
  plot_legend = FALSE,
  colors_use = NULL,
  color_seed = 123,
  ggplot_default_colors = FALSE,
  plot_spacing = 0.15,
  spacing_unit = "cm",
  vln_linewidth = NULL,
  pt.size = NULL,
  raster = NULL,
  add.noise = TRUE,
  ...
)

Arguments

seurat_object

Seurat object name.

features

Features to plot.

group.by

Group (color) cells in different ways (for example, orig.ident).

split.by

A variable to split the violin plots by,

idents

Which classes to include in the plot (default is all).

x_lab_rotate

logical or numeric. If logical whether to rotate x-axis labels 45 degrees (Default is FALSE). If numeric must be either 45 or 90. Setting 45 is equivalent to setting TRUE.

plot_legend

logical. Adds plot legend containing idents to the returned plot.

colors_use

specify color palette to used in VlnPlot. 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.

color_seed

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

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.

plot_spacing

Numerical value specifying the vertical spacing between each plot in the stack. Default is 0.15 ("cm"). Spacing dependent on unit provided to spacing_unit.

spacing_unit

Unit to use in specifying vertical spacing between plots. Default is "cm".

vln_linewidth

Adjust the linewidth of violin outline. Must be numeric.

pt.size

Adjust point size for plotting. Default for Stacked_VlnPlot is 0 to avoid issues with rendering so many points in vector form. Alternatively, see raster parameter.

raster

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).

add.noise

logical, determine if adding a small noise for plotting (Default is TRUE).

...

Extra parameters passed to VlnPlot.

Value

A ggplot object

Author

Ming Tang (Original Code), Sam Marsh (Wrap single function, added/modified functionality)

Examples

library(Seurat)
Stacked_VlnPlot(seurat_object = pbmc_small, features = c("CD3E", "CD8", "GZMB", "MS4A1"),
x_lab_rotate = TRUE)
#> Warning: The following features were omitted as they were not found:
#> ℹ CD8