Single cell violin plot

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

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

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.

Arguments

Value

See also

Examples