rdiAxis - RDI Axis annotation function
This function takes a RDI model, as generated by rdiModel, and adds an axis with annotations in the fold change space.
rdiAxis(model, side = 2, at = NULL, ...)
- A model object, as generated by rdiModel.
- The side the axis will be added to. (1 - bottom; 2 - left; 3 - top; 4 - right). Default is 2.
- The points at which the tick marks are drawn. By default, tickmarks are placed at ‘round’ fold/percent change values using the “pretty” breakpoints function. This may not be ideal if log-RDI values are being plotted.
- Additional parameters to pass to axis
This function is designed to replace the default axes generated by a plot
function. Instead of annotating the true RDI value,
rdiAxis will estimate
the “true difference” values at various points within the plotting region, and will
annotate the axis with those estimates.
It is worth noting that although the RDI value can range below
estimate for “identical” repertoires, no negative true difference values will be
annotated, as these values do not make sense.
#create genes genes = sample(letters, 10000, replace=TRUE) #create sequence annotations seqAnnot = data.frame(donor = sample(1:10, 10000, replace=TRUE)) #calculate RDI d = rdi(genes, seqAnnot) ##create a "baseVect" with the same probability as our features ##since we sampled uniformly, the base vector has equal probability baseVect = rep(1/length(letters),length(letters)) ##generate an RDI model m = rdiModel(attr(d, "nseq"), baseVects=baseVect) ##convert RDI to lfc td = convertRDI(d,models=m)$pred par(mar=c(4,4,1,4),las=1,mgp=c(3,0.5,0)) plot(td,d, ylab="RDI", xlab="LFC")
##now add "true difference" axis annotation to the right side of the plot rdiAxis(m, side=4)