plot.wildtype_mutant_pnpp {ddpcr}R Documentation

Plot a ddPCR plate of type wildtype/mutant PNPP

Description

Same plot as plot.pnpp_experiment but with a few extra features that are specific to wildtype/mutant PNPP plates. Take a look at plot.pnpp_experiment to see all supported parameters and more information.

Usage

## S3 method for class 'wildtype_mutant_pnpp'
plot(
  x,
  wells,
  samples,
  ...,
  col_drops_mutant = "purple3",
  col_drops_wildtype = "green3",
  col_drops_rain = "black",
  show_mutant_freq = TRUE,
  text_size_mutant_freq = 4,
  alpha_drops_low_mutant_freq = 0.5,
  show_low_high_mut_freq = TRUE,
  bg_mutant = "purple3",
  bg_wildtype = "green3",
  alpha_bg_low_high_mut_freq = 0.1
)

Arguments

x

A ddPCR plate.

wells

Only plot selected wells. Supports range notation, see subset.ddpcr_plate.

samples

Only plot selected samples.

...

Parameters to pass to plot.pnpp_experiment.

col_drops_mutant

The colour to use for mutant droplets.

col_drops_wildtype

The colour to use for wildtype droplets.

col_drops_rain

The colour to use for rain droplets.

show_mutant_freq

If TRUE, show the mutant frequency as a percentage on each well.

text_size_mutant_freq

Text size of the printed mutant frequencies.

alpha_drops_low_mutant_freq

Transparency of mutant droplets in wells with mostly wildtype droplets. In wells where there are very few mutant droplets, it might be useful to make them more visible by increasing their transparency.

show_low_high_mut_freq

Differentiate between wells with a high vs low mutant frequency by having a different background colour to the well.

bg_mutant

The background colour for wells that have a significant mutant cluster.

bg_wildtype

The background colour for wells that have mostly wildtype drops.

alpha_bg_low_high_mut_freq

The transparency value for bg_mutant and bg_wildtype.

Value

A ggplot2 plot object.

See Also

plot.ddpcr_plate
plot.pnpp_experiment
wildtype_mutant_pnpp

Examples

## Not run: 
plate <- new_plate(sample_data_dir(), type = plate_types$fam_positive_pnpp) %>% analyze
wells_wildtype(plate)
plot(plate)
plate <- plate %>% analyze
plot(plate)
plot(plate, "A01:C05", col_drops_rain = "blue")

## End(Not run)

[Package ddpcr version 1.15 Index]