plot_demultiplex {scPipe} | R Documentation

## plot_demultiplex

### 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)

[Package scPipe version 1.2.1 Index]