Hi, 

Is it possible to draw a heatmap with plotPlaid from some (or all) chromosomes together? How?

No, it's not possible to do that. The plotPlaid function requires one genomic interval on the x- and y-axes. This means you can't specify multiple chromosomes, because that doesn't fit into a single GRanges entry.

Personally, I don't find multi-chromosome plaid plots to be particularly interesting. You get boxes along the diagonal for the strong intra-chromosomal contacts, and nothing much else. There are some exceptions, e.g., yeast data where centromeres of different chromosomes interact with each other, or cancer cell lines with translocations. But in general, most of the inter-chromosomal space is pretty empty and boring to look at.

If you really need it, you could probably mimic it with something like:

all.chrs <- range(param$fragments)
nchrs <- length(all.chrs)
par(mfrow=c(nchrs, nchrs))
for (x in all.chrs) {
    for (y in all.chrs) {
        plotPlaid("myfile.h5", param, x, y) # plot between current chr pair
    }
}

This will make a plot of nchrs by nchrs subplots, where each subplot represents the plot between two chromosomes. You could probably get it looking reasonably nice by reducing the margins for each plot (using mar= in par) to cut down the whitespace.