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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$features is a list, it will run RunSeuratDEAnalysis() to get the markers for each group, and then select the top n/ngroups features for each group based on the order field. If RunUMAPArgs$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))". RunUMAPArgs$from can be a path to a TSV file containing pre-computed UMAP coordinates to overwrite the results of Seurat::RunUMAP(). The path should be in the format "file:///path/to/file#id_col,coord_col1,coord_col2", where id_col is the column with cell barcodes and the remaining columns are the UMAP coordinate columns (e.g., UMAP_1,UMAP_2). The cell barcodes must match those in the Seurat object, and the coordinate column names must match the reduction's cell.embeddings column names. You can also use 1-based column indices instead of names, e.g., "file:///path/to/file#1,2,3".

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").