plot_demultiplex: plot_demultiplex

In scPipe: pipeline for single cell RNA-seq data analysis

Description

Plot cell barcode demultiplexing result for the SingleCellExperiment. The barcode demultiplexing result is shown using a barplot, with the bars indicating proportions of total reads. Barcode matches and mismatches are summarised along with whether or not the read mapped to the genome. High proportion of genome aligned reads with no barcode match may indicate barcode integration failure.

Usage

plot_demultiplex(sce)

Arguments

sce	a SingleCellExperiment object

Value

a ggplot2 bar chart

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

plot_demultiplex(sce)

scPipe documentation built on Nov. 8, 2020, 8:28 p.m.