Single cell violin plot

Source: R/visualization.R

Draws a violin plot of single cell data (gene expression, metrics, PC scores, etc.)

VlnPlot(
  object,
  features,
  cols = NULL,
  pt.size = NULL,
  idents = NULL,
  sort = FALSE,
  assay = NULL,
  group.by = NULL,
  split.by = NULL,
  adjust = 1,
  y.max = NULL,
  same.y.lims = FALSE,
  log = FALSE,
  ncol = NULL,
  slot = "data",
  split.plot = FALSE,
  stack = FALSE,
  combine = TRUE,
  fill.by = "feature",
  flip = FALSE,
  raster = NULL
)

Arguments

object

Seurat object
features

Features to plot (gene expression, metrics, PC scores, anything that can be retreived by FetchData)
cols

Colors to use for plotting
pt.size

Point size for geom_violin
idents

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

Sort identity classes (on the x-axis) by the average expression of the attribute being potted, can also pass 'increasing' or 'decreasing' to change sort direction
assay

Name of assay to use, defaults to the active assay
group.by

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

A variable to split the violin plots by,
adjust

Adjust parameter for geom_violin
y.max

Maximum y axis value
same.y.lims

Set all the y-axis limits to the same values
log

plot the feature axis on log scale
ncol

Number of columns if multiple plots are displayed
slot

Use non-normalized counts data for plotting
split.plot

plot each group of the split violin plots by multiple or single violin shapes.
stack

Horizontally stack plots for each feature
combine

Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot
fill.by

Color violins/ridges based on either 'feature' or 'ident'
flip

flip plot orientation (identities on x-axis)
raster

Convert points to raster format. Requires 'ggrastr' to be installed.

Value

A patchworked ggplot object if combine = TRUE; otherwise, a list of ggplot objects

See also

FetchData

Examples

data("pbmc_small")
VlnPlot(object = pbmc_small, features = 'PC_1')

VlnPlot(object = pbmc_small, features = 'LYZ', split.by = 'groups')

#> The default behaviour of split.by has changed.
#> Separate violin plots are now plotted side-by-side.
#> To restore the old behaviour of a single split violin,
#> set split.plot = TRUE.
#>       
#> This message will be shown once per session.