plot_props_alluvial: Plot grouped alluvial plots of cell type proportions

In maple: Bayesian Analysis of Multi-Sample Spatial Transcriptomics Experiments

Plot grouped alluvial plots of cell type proportions

Description

This function allows you to visualize the relative abundance of sub-populations after running fit_maple()

Usage

plot_props_alluvial(fit, group)

Arguments

fit	A list returned by fit_maple()
group	A column name of fit$W or a grouping vector of length N (nrow(fit$W))

Value

A ggplot object

Examples

## Not run: 
brain1 <- LoadData("stxBrain", type = "anterior1")
brain2 <- LoadData("stxBrain", type = "anterior2")
brain1 <- SCTransform(brain1, assay = "Spatial", verbose = FALSE)
brain2 <- SCTransform(brain2, assay = "Spatial", verbose = FALSE)
brain <- merge(brain1,brain2)
DefaultAssay(brain) <- "SCT"
VariableFeatures(brain) <- c(VariableFeatures(brain1),VariableFeatures(brain2))
brain <- RunPCA(brain)
brain_fit_PCs <- fit_maple(brain,K = 6,emb = "PCs")
plot_props_alluvial(brain_fit_PCs, group = brain$orig.ident)

## End(Not run)

maple documentation built on March 18, 2022, 6:02 p.m.