DetectedAI-plot: DetectedAI plot

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description

plot functions for the DetectedAI-class

Usage

frequency_vs_threshold_variable_plot(x, ...)

## S4 method for signature 'DetectedAI'
frequency_vs_threshold_variable_plot(
  x,
  var = "threshold.count.sample",
  hetOverlay = TRUE,
  smoothscatter = FALSE
)

detectedAI_vs_threshold_variable_plot(x, ...)

## S4 method for signature 'DetectedAI'
detectedAI_vs_threshold_variable_plot(
  x,
  var = "threshold.count.sample",
  summaryOverSamples = "sum",
  hetOverlay = TRUE,
  smoothscatter = FALSE
)

reference_frequency_density_vs_threshold_variable_plot(x, ...)

## S4 method for signature 'DetectedAI'
reference_frequency_density_vs_threshold_variable_plot(
  x,
  var = "threshold.count.sample"
)

detectedAI_vs_threshold_variable_multigraph_plot(x, ...)

## S4 method for signature 'DetectedAI'
detectedAI_vs_threshold_variable_multigraph_plot(x, ncol = 2, ...)

frequency_vs_threshold_variable_multigraph_plot(x, ...)

## S4 method for signature 'DetectedAI'
frequency_vs_threshold_variable_multigraph_plot(x, ncol = 2, ...)

reference_frequency_density_vs_threshold_variable_multigraph_plot(x, ...)

## S4 method for signature 'DetectedAI'
reference_frequency_density_vs_threshold_variable_multigraph_plot(
  x,
  ncol = 2,
  ...
)

Arguments

x	detectedAI object
...	pass on variables internally
var	string, see details for available options
hetOverlay	logical, if TRUE show nr of het SNPs used to calculate the reference allele frequency mean
smoothscatter	boolean, smoothscatter over the means
summaryOverSamples	'mean' or 'sum'
ncol	nr of columns for multiplots

Details

plot helper functions. The documentation will be improved before next release.

Author(s)

Jesper R. Gadin, Lasse Folkersen

Examples

#some example code here
#generate example
data(ASEset)
a <- ASEset
dai <- detectAI(a, 
			threshold.count.sample=1:50,
			threshold.frequency=seq(0,0.5,by=0.01),
			threshold.delta.frequency=seq(0,0.5,by=0.01),
			threshold.pvalue=rev(seq(0.001,0.05, by=0.005))
)

frequency_vs_threshold_variable_plot(dai)
detectedAI_vs_threshold_variable_plot(dai)
detectedAI_vs_threshold_variable_multigraph_plot(dai)
frequency_vs_threshold_variable_multigraph_plot(dai)

pappewaio/AllelicImbalance documentation built on April 11, 2020, 2:58 a.m.