QCPlot: Generate a QC plot from Seurat metadata

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

Generate a QC plot from Seurat metadata

Description

This function generates a series of box plots as quality control for a Seurat object

Usage

QCPlot(
  seurat_obj,
  y_elements = c("nCount_RNA", "nFeature_RNA", "percent.mt"),
  group_by = "seurat_clusters",
  y_lab = c("UMI Count", "Gene Count", "% MT"),
  x_lab = "Cluster ID",
  stage = "orig.ident",
  quantiles = c(0.25, 0.75),
  ...
)

Arguments

seurat_obj	Seurat object
y_elements	[e-mail] column to plot QC metrics for
group_by	[e-mail] column to group cells by on x axis
y_lab	array of labels for y axis reflecting y_elements
x_lab	label for x axis
stage	[e-mail] column to stack cell count bars by
quantiles	Percent quantiles to plot on bar plots. Can be either NULL, a single element, or an array (length 2) with lower and upper percent
...	Extra arguments to be passed to grid.arrange

Value

plot output from grid.arrange

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