removeCellsByUmap: Remove Cells by Dimension Reduction

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Remove Cells by Dimension Reduction

Description

This function applies a cutoff in the specified dimension of a given dimension reduction (UMAP, PCA, or t-SNE) to remove cells.

Usage

removeCellsByUmap(
  reduction = "umap",
  umap_dim = 1,
  obj = combined.obj,
  cutoff = 0,
  cut_below = TRUE,
  only_plot_cutoff = FALSE,
  ...
)

Arguments

reduction	A string specifying the dimension reduction technique to be used ('umap', 'pca', or 'tsne'). Default: 'umap'.
umap_dim	An integer specifying which dimension (axis) to apply the cutoff. Default: 1.
obj	A Seurat object. Default: 'combined.obj'.
cutoff	A numerical value indicating the cutoff value for the specified dimension. Default: 0.
cut_below	A logical value indicating whether to remove cells below (TRUE) or above (FALSE) the cutoff line. Default: TRUE.
only_plot_cutoff	Simulate and plot cutoff only.
...	Any other parameters to be passed to internally called functions.

Value

A Seurat object with cells removed according to the specified cutoff.

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.