plotDensity: plotDensity

In liuqivandy/scRNABatchQC: a package for quality control of multiple single cell RNAseq data

Description

plot the distribution of total_counts, total_features, pct_counts_Mt (percentage of mtRNA counts) or pct_counts_rRNA (percentage of rRNA counts) for multiple single cell RNAseq datasets

Usage

plotDensity(
  sces,
  feature = c("total_counts", "total_features", "pct_counts_Mt", "pct_counts_rRNA"),
  featureLabel = NULL,
  scolors = 1:length(sces),
  lineSize = 1
)

Arguments

sces	a list of SingleCellExperiment objects; each object containing QC metadata for each dataset; (results from Process_scRNAseq )
feature	string; which features to plot; features can be total_counts, total_features, pct_counts_Mt, pct_counts_rRNA; (default: total_counts)
featureLabel	string; label of feature
scolors	vector of color
lineSize	integer; size of line

See Also

Process_scRNAseq

Examples

library(scRNABatchQC)
sces<-Process_scRNAseq(inputfiles=c("https://github.com/liuqivandy/scRNABatchQC/raw/master/bioplar1.csv.gz",
                                    "https://github.com/liuqivandy/scRNABatchQC/raw/master/bioplar5.csv.gz"))
                
plotDensity(sces,"total_counts")
# plot the total counts distribution of the first dataset
plotDensity(sces[1],"total_counts")

liuqivandy/scRNABatchQC documentation built on March 24, 2021, 11:01 p.m.