UmiCountsPlot {umiAnalyzer}

Plot UMI counts

Description

Visualize the number detected UMI for each consensus depth cut-off. This may may helpful in choosing the right consensus depth for your analysis, by checking the number of reads still available for each assay and sample for your chosen cut-off.

Usage

UmiCountsPlot(
  object,
  amplicons = NULL,
  samples = NULL,
  theme = "classic",
  option = "viridis",
  direction = 1
)

Arguments

object

Requires a UMI sample or UMI experiment object

amplicons

(Optional) user-supplied list of assays to plot. Default is all.

samples

(Optional) user-supplied list of samples to plot. Default is all.

theme

Plotting theme, default is classic

option

Color palette. Default uses ggplot standard, otherwise viridis options.

direction

If using viridis colors should the scale be inverted or default?

Value

A UMIexperiment object

Examples

library(umiAnalyzer)

main = system.file('extdata', package = 'umiAnalyzer')
samples <- list.dirs(path = main, full.names = FALSE, recursive = FALSE)
simsen <- createUmiExperiment(experimentName = 'example',mainDir = main,sampleNames = samples)
simsen <- filterUmiObject(simsen)

count_plot <- UmiCountsPlot(simsen)