VlnPlot: Single cell violin plot

In Seurat: Tools for Single Cell Genomics

Single cell violin plot

Description

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

Usage

VlnPlot(
  object,
  features,
  cols = NULL,
  pt.size = NULL,
  alpha = 1,
  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 = deprecated(),
  layer = NULL,
  split.plot = FALSE,
  stack = FALSE,
  combine = TRUE,
  fill.by = "feature",
  flip = FALSE,
  add.noise = TRUE,
  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 points
alpha	Alpha value for points
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 factor in object metadata to split the plot by, pass 'ident' to split by cell identity'
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	Slot to pull expression data from (e.g. "counts" or "data")
layer	Layer to pull expression data from (e.g. "counts" or "data")
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)
add.noise	determine if adding a small noise for plotting
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')

Seurat documentation built on May 29, 2024, 4:20 a.m.