AllelicImbalance (version 1.10.2)

DetectedAI-plot: DetectedAI plot

Description

plot functions for the DetectedAI-class

Usage

frequency_vs_threshold_variable_plot(x, ...)
"frequency_vs_threshold_variable_plot"(x, var = "threshold.count.sample", hetOverlay = TRUE, smoothscatter = FALSE)
detectedAI_vs_threshold_variable_plot(x, ...)
"detectedAI_vs_threshold_variable_plot"(x, var = "threshold.count.sample", summaryOverSamples = "sum", hetOverlay = TRUE, smoothscatter = FALSE)
reference_frequency_density_vs_threshold_variable_plot(x, ...)
 "reference_frequency_density_vs_threshold_variable_plot"(x, var = "threshold.count.sample")
detectedAI_vs_threshold_variable_multigraph_plot(x, ...)
"detectedAI_vs_threshold_variable_multigraph_plot"(x, ncol = 2, ...)
frequency_vs_threshold_variable_multigraph_plot(x, ...)
"frequency_vs_threshold_variable_multigraph_plot"(x, ncol = 2, ...)
reference_frequency_density_vs_threshold_variable_multigraph_plot(x, ...)
 "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.

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)