View source: R/visualization.R
CollapseEmbeddingOutliers | R Documentation |
Move outliers towards center on dimension reduction plot
CollapseEmbeddingOutliers(
object,
reduction = "umap",
dims = 1:2,
group.by = "ident",
outlier.sd = 2,
reduction.key = "UMAP_"
)
object |
Seurat object |
reduction |
Name of DimReduc to adjust |
dims |
Dimensions to visualize |
group.by |
Group (color) cells in different ways (for example, orig.ident) |
outlier.sd |
Controls the outlier distance |
reduction.key |
Key for DimReduc that is returned |
Returns a DimReduc object with the modified embeddings
## Not run:
data("pbmc_small")
pbmc_small <- FindClusters(pbmc_small, resolution = 1.1)
pbmc_small <- RunUMAP(pbmc_small, dims = 1:5)
DimPlot(pbmc_small, reduction = "umap")
pbmc_small[["umap_new"]] <- CollapseEmbeddingOutliers(pbmc_small,
reduction = "umap", reduction.key = 'umap_', outlier.sd = 0.5)
DimPlot(pbmc_small, reduction = "umap_new")
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.