plot_QC_pairs: Plot GGAlly pairs plot of QC statistics from...
In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

plot_QC_pairs

R Documentation

Plot GGAlly pairs plot of QC statistics from `SingleCellExperiment` object

Description

Plot GGAlly pairs plot of QC statistics from SingleCellExperiment object

Usage

plot_QC_pairs(sce, sel_col = NULL)

Arguments

`sce`	a `SingleCellExperiment` object
`sel_col`	a vector of column names which indicate the columns to use for plot. By default it will be the statistics generated by 'calculate_QC_metrics()'

Value

a ggplot2 object

Examples

data("sc_sample_data")
data("sc_sample_qc")
sce = SingleCellExperiment(assays = list(counts = as.matrix(sc_sample_data)))
organism(sce) = "mmusculus_gene_ensembl"
gene_id_type(sce) = "ensembl_gene_id"
QC_metrics(sce) = sc_sample_qc
demultiplex_info(sce) = cell_barcode_matching
UMI_dup_info(sce) = UMI_duplication
sce = detect_outlier(sce)

plot_QC_pairs(sce)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.