plot_mapping: Plot mapping statistics for 'SingleCellExperiment' object.

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

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")

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