plot_mapping: Plot mapping statistics for 'SingleCellExperiment' object.

View source: R/qc.R

plot_mappingR Documentation

Plot mapping statistics for SingleCellExperiment object.

Description

Plot mapping statistics for SingleCellExperiment object.

Usage

plot_mapping(sce, sel_col = NULL, percentage = FALSE, dataname = "")

Arguments

sce

a SingleCellExperiment object

sel_col

a vector of column names, indicating the columns to use for plot. by default it will be the mapping result.

percentage

TRUE to convert the number of reads to percentage

dataname

the name of this dataset, used as plot title

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

plot_mapping(sce,percentage=TRUE,dataname="sc_sample")


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