DepthPlot: Plot genes detected vs. nUMI

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

Description

Plot genes detected vs. nUMI

Usage

DepthPlot(
  E,
  Cutoffs = NULL,
  Barcodes = NULL,
  show.min_genes = T,
  show.min_umi = T,
  print.pdf = T,
  fn = "DepthPlots.pdf"
)

Arguments

E	Count matrix (see ?Read_h5)
Cutoffs	A dataframe as returned by ?GetCutoffs
Barcodes	A list as returned by ?FilterBackgroundMatrix or ?GetBackgroundMatrix
show.min_genes	If TRUE, plot a line with the minimum gene cutoff
show.min_umi	If TRUE, plot a line with the minimum nUMI cutoff
print.pdf	If TRUE, returns "DepthPlots.pdf" in the working directory. Default is TRUE.
fn	Filename of the .pdf file. Default is "DepthPlots.pdf".

Value

PDF where each page is a plot of the genes detected vs. nUMI, or a list of ggplot objects.

See Also

DepthPlotComparison, GetCutoffs

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