maple_viz: Plot tissue architecture labels

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

Plot tissue architecture labels

Description

This function allows you to plot (static or interactive) cell spot labels and uncertainty measures

Usage

maple_viz(
  fit,
  pt.size = 1,
  interactive = FALSE,
  shade_uncertainty = FALSE,
  feature = NULL
)

Arguments

fit	A list returned by fit_maple()
pt.size	The size of each cell spot point
interactive	Logical parameter controlling static or interactive nature of plot
shade_uncertainty	Logical parameter for shading of cell spots by posterior uncertainty. Must run get_maple_scores() first.
feature	A user-provided feature (e.g., gene of interest) to visualize over tissue spaces instead of sub-population labels.

Value

A ggplot object or shiny app window

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")
maple_viz(brain_fit_PCs)

## End(Not run)

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