You can change the distance between chromosomes as well as the height of the ideogram or the data panels using the "plot.params" argument in
In your case you'll probably want to increase the value of
data1outmargin but there are many different parameters to adjust. You can see them all calling
plotDefaultPlotParams and giving it the plot type you are using. For example, for plot type 2 you would get something like this.
This function can even receive a
plot.params object and it will adjust itself to plot the given parameters to help you understand the plotting process. I've used that many times.
Oh, and I usually recommend creating big images (at least 1500x1500 or 2000x2000 px pngs). This also helps you get a clearer picture of the data you have.
Hope this helps,