filtDistClst: Filter singleton cells from the UMAP embedding by distance...

In plantformatics/Socrates: Analysis of scATAC-seq data

Filter singleton cells from the UMAP embedding by distance per cluster

Description

This function removes cells from the UMAP embedding that are not well supported by other cells. Can be run on a per cluster basis to filter cells that exceed a heuristic threshold of distances to most other cells in the same cluster.

Usage

filtDistClst(b, umap1 = "umap1", umap2 = "umap2", threshold2 = 2)

Arguments

b	meta data after clustering with Seurat
threshold2	numeric, Z-score threshold to remove cells greater than X standard standard deviations from other cells.
m1	character, if type=="umap", then set to the column name of first component ("umap1"). Only used when running sub-clustering (umap embedding names for subset and regenerated UMAP embeddings of a subset of cells).
m2	character, if type=="umap", then set to the column name of second component ("umap2"). #' Only used when running sub-clustering (umap embedding names for subset and regenerated UMAP embeddings of a subset of cells).

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.