QCPlots: Plot total genes and total counts histograms

In mathewchamberlain/veni: Generates QC plots, performs ambient RNA removal, and enhanced differential from single cell RNA sequencing data

Description

Plot total genes and total counts histograms

Usage

QCPlots(
  E,
  print.pdf = T,
  QC = c("Genes detected", "Total counts", "Mito")[1],
  order.by = c("average depth", "mito percentage")[1],
  fn = "default",
  choose = c("Mito", "all")[1],
  min_counts = 100,
  min_genes = 100
)

Arguments

E	Count matrix (see ?Read_h5)
print.pdf	If TRUE, returns pdf files in the working directory. Default is TRUE; if FALSE, returns list of ggplot2 objects.
QC	Type of QC plot, "Genes Detected", "Total Counts" or "Mito". Default is Genes Detected.
order.by	Order by a quantity associated with each sample. Options are "average depth" or "mito percentage", default is AvgDepth.
fn	Filename of the .pdf file. Default is the input parameter QC saved as a .pdf file.
choose	See ?FilterMito or ?GetMito
min_counts	Keep cells with at least min_counts, default is 100.
min_genes	Keep cells with at least min_genes, default is 100.

Value

PDF, histogram of total counts, or a list of ggplot objects.

See Also

DepthPlot; DepthPlotComparison

mathewchamberlain/veni documentation built on Oct. 9, 2020, 2:30 a.m.