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Run seurat UMAP

Source: R/scrna-macros.R
RunSeuratUMAP.Rd

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.

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