Alluvial plot from a Seurat object

Aggregate cell counts by any two metadata fields and draw an alluvial plot with plot_alluvial. Extra arguments are passed straight to plot_alluvial().

Usage

plot_alluvial_sc(
  obj,
  group_col = "Group",
  cluster_col = "Cluster",
  return = "plot",
  ...
)

Arguments

obj

A Seurat object.

group_col

Metadata field mapped to the x-axis (e.g. sample, time).

cluster_col

Metadata field defining strata (e.g. cell type / ident).

return

return a plot (set "plot") or a list with plot and data (set "both").

...

Additional arguments forwarded to plot_alluvial().

Value

A ggplot2 object.

Examples

library(Seurat)
data("pbmc_small")
pbmc_small$Group   <- pbmc_small$orig.ident   # mock group
pbmc_small$Cluster <- Idents(pbmc_small)      # use idents

## default colours
plot_alluvial_sc(pbmc_small)


## custom palette (unnamed)
plot_alluvial_sc(
  pbmc_small,
  palette = c("#8DD3C7","#FFFFB3","#BEBADA","#FB8072",
              "#80B1D3","#FDB462","#B3DE69"))