Hi Alice,
I was able to take another look at this today. The sorting based on the mapping file column doesn't work exactly as you (and I) were thinking. This is intended to be used with a categorical variable, not a continuous variable, so your order column won't work for this.
I think what you're trying to do is sort the samples on the horizontal axis of your heatmap based on the "ORDER" column in your sample metadata file. To do this, you should use the -m option to make_otu_heatmap.py without the -c option (see the usage examples when you call make_otu_heatmap.py -h). The mapping file that you pass should be sorted in the reverse order that you want the samples to appear (there appears to be a bug in the script, where the first samples in the mapping file will be the rightmost samples on the horizontal axis of the heatmap).
I've attached the mapping file that I created for this. The command I ran was as follows:
make_otu_heatmap.py -i g23_abund.biom -o g23_abund.pdf -m g23-mapping2.txt
I've also attached the resulting heatmap.
Sorry for the trouble, I hope this gets you what you need!
Best,
Greg