visualize associations between two groups of data

Question

Where each datapoint has a pairing of A and B and there multiple entries in A and multiple entires in B. IE multiple syndromes and multiple diagnoses, although for each data

Answer 1

Since your data is bipartite, I would suggest plotting points in the first factor on one side, points in the other factor on the other, with lines between them, like so:

The code I used to generate this was:

## Make up data.
data <- data.frame(X1=sample(state.region, 10),
                   X2=sample(state.region, 10))

## Set up plot window.
plot(0, xlim=c(0,1), ylim=c(0,1),
     type="n", axes=FALSE, xlab="", ylab="")

factor.to.int <- function(f) {
  (as.integer(f) - 1) / (length(levels(f)) - 1)
}

segments(factor.to.int(data$X1), 0, factor.to.int(data$X2), 1,
         col=data$X1)
axis(1, at = seq(0, 1, by = 1 / (length(levels(data$X1)) - 1)),
     labels = levels(data$X1))
axis(3, at = seq(0, 1, by = 1 / (length(levels(data$X2)) - 1)),
     labels = levels(data$X2))