DepthPlot: Plot genes detected vs. nUMI

Description Usage Arguments Value See Also

View source: R/veni.R

Description

Plot genes detected vs. nUMI

Usage

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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


sanofi-pi/veni documentation built on Oct. 12, 2020, 10:17 p.m.