AmpliconPlot {umiAnalyzer}

Generate Amplicon plots

Description

Plots variant allele frequencies or alternate allele counts for chosen samples and assays.

Usage

AmpliconPlot(
  object,
  filter.name = "default",
  cut.off = 5,
  min.count = 0,
  min.vaf = 0,
  amplicons = NULL,
  samples = NULL,
  abs.count = FALSE,
  y_min = 0,
  y_max = NULL,
  theme = "classic",
  option = "default",
  direction = "default",
  plot.text = FALSE,
  plot.ref = TRUE,
  stack.plot = FALSE,
  classic.plot = FALSE,
  fdr = 0.05,
  font.size = 6,
  angle = 45,
  use.caller = FALSE,
  use.plotly = TRUE
)

Arguments

object

Requires a UMI sample or UMI experiment object

filter.name

Name of the filter to be plotted.

cut.off

How many variant reads are necessary to consider a variant above background? Default is 5 reads.

min.count

Minimum variants counts to plot, default is 0.

min.vaf

Minimum variants allele frequency to plot, default is 0.

amplicons

(Optional) character vector of amplicons to be plotted.

samples

(Optional) character vector of samples to be plotted.

abs.count

Should absolute counts be plotted instead of frequencies? Default is FALSE.

y_min

Minimum y-axis value, default is 0

y_max

Maximum y-axis value, default is NULL (autoscale)

theme

Plotting theme to use, default is classic.

option

Color palette to use.

direction

Orientation of the color palette.

plot.text

Should non-references bases be indicated above the bar?

plot.ref

If true show reference base instead of position on x-axis.

stack.plot

Show all variant alleles in a stacked bar plot.

classic.plot

Show classical debarcer amplicon plot with raw error.

fdr

False-discovery-rate cut-off for variants.

font.size

Font size

angle

Font angle

use.caller

Should data from variant caller be used? Default is FALSE

use.plotly

Should plotly be used instead of the regular ggplot device? Default is TRUE

Value

A UMIexperiment object containing a ggplot object with the amplicon plot.

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)

amplicon_plot <- AmpliconPlot(simsen)