DetectedAI-plot {AllelicImbalance} | R Documentation |
plot functions for the DetectedAI-class
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, ... )
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 |
plot helper functions. The documentation will be improved before next release.
Jesper R. Gadin, Lasse Folkersen
#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)