Is there any way to sort the order of samples when using the heatmap.bin command?
Okay - I found one way to do it. The output is displayed according to the order in which the first sequence from each group is read in from the *.group file. If you go in and manually bring one sequence of each group to the top of the *.group file, you can arrange the input order of the first sequence from each group however you want.
In version 1.12.0, the read.otu command will sort the groups alphabetically by default or you will be able to add a ordergroup file containing your groups in the order you would like.