maple_viz | R Documentation |
This function allows you to plot (static or interactive) cell spot labels and uncertainty measures
maple_viz( fit, pt.size = 1, interactive = FALSE, shade_uncertainty = FALSE, feature = NULL )
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. |
A ggplot object or shiny app window
## 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)
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