DetectedAI-plot {AllelicImbalance} | R Documentation

## DetectedAI plot

### 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)

[Package AllelicImbalance version 1.32.0 Index]