CheckIntegration: Check Integration

In alexthiery/scHelper: R package containing helper functions for single cell analysis

Check Integration

Description

This function plots UMAPs after integration, allowing you to see that cells from the same population but sequenced as part of separate batches, overlap after integration.

Usage

CheckIntegration(
  seurat_object,
  group_by = "orig.ident",
  split_chr = "-",
  pt.size = 0.2,
  xlim = c(-15, 15),
  ylim = c(-15, 15),
  nrow = 1,
  shuffle = TRUE,
  seed = 123,
  title = "all cells"
)

Arguments

seurat_object	Seurat object
group_by	[e-mail] column to group cells by - this should correspond to the variable which identifies shared populations across batches
split_chr	character or string used to split group_by variable by batch (i.e. for 'hh6-1' you should specify '-')
nrow	number of rows to pass to grid.arrange
shuffle	randomly plot cells in order to prevent hiding certain populations when overplotting
seed	set seed for plotting consistency when shuffle is TRUE
title	title for plot displaying all cells

Value

plot generated by grid arrange

alexthiery/scHelper documentation built on Aug. 26, 2023, 3:42 p.m.