Run seurat UMAP

In additional to Seurat::RunUMAP(), we provide an additional arguments to use markers as features for UMAP, which makes the UMAP more separated for different clusters.

Usage

RunSeuratUMAP(object, RunUMAPArgs = list(), cache = NULL, log = NULL)

Arguments

object

Seurat object

RunUMAPArgs

Arguments to pass to Seurat::RunUMAP(). RunUMAPArgs$features can be a character vector of features directly used for UMAP, or a list with the following fields:

• order: The order of the markers to use for UMAP, e.g. "desc(abs(avg_log2FC))"

• n: The number of total features to use for UMAP, e.g. 30 If RunUMAPArgs$features is a list, it will run RunSeuratDEAnalysis() to get the markers for each group, and then select the top n/ngroups features for each group based on the order field. If RunUMAPArgs$features is a numeric value, it will be treated as the n field in the list above, with the default order being "desc(abs(avg_log2FC))".

cache

Directory to cache the all markers, which can be reused later if DE analysis is desired.

log

The logger to use. If NULL, a default logger will be used.

Value

The Seurat object with UMAP results

Details

When both RunUMAPArgs$features and RunUMAPArgs$dims are provided, RunUMAPArgs$dims will be ignored. If neither RunUMAPArgs$features nor RunUMAPArgs$dims is provided, RunUMAPArgs$dims will be set to 1:min(30, ceiling(ncells/3), ncol(object@reductions[[reduction]])), where ncells is the number of cells in the object, and reduction is RunUMAPArgs$reduction (default: "pca").