QC_Histogram: QC Histogram Plots

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

QC Histogram Plots

Description

Custom histogram for initial QC checks including lines for thresholding

Usage

QC_Histogram(
  seurat_object,
  features,
  low_cutoff = NULL,
  high_cutoff = NULL,
  cutoff_line_width = NULL,
  split.by = NULL,
  bins = 250,
  colors_use = "dodgerblue",
  num_columns = NULL,
  plot_title = NULL,
  assay = NULL,
  print_defaults = FALSE
)

Arguments

seurat_object	Seurat object name.
features	Feature from meta.data, assay features, or feature name shortcut to plot.
low_cutoff	Plot line a potential low threshold for filtering.
high_cutoff	Plot line a potential high threshold for filtering.
cutoff_line_width	numerical value for thickness of cutoff lines, default is NULL.
split.by	Feature to split plots by (i.e. "orig.ident").
bins	number of bins to plot default is 250.
colors_use	color to fill histogram bars, default is "dodgerblue".
num_columns	Number of columns in plot layout.
plot_title	optional, vector to use for plot title. Default is the name of the variable being plotted.
assay	assay to pull features from, default is active assay.
print_defaults	return list of accepted default shortcuts to provide to features instead of full name.

Value

A patchwork object

Examples

## Not run: 
QC_Histogram(seurat_object = object, features = "nFeature_RNA")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.