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 )
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 |
fill.by | Color violins/ridges based on either 'feature' or 'ident' |
flip | flip plot orientation (identities on x-axis) |
A patchworked
ggplot object if combine = TRUE
; otherwise, a list of ggplot objects
VlnPlot(object = pbmc_small, features = 'LYZ', split.by = 'groups')#>#> #> #> #> #>