I'm having a problem with my otu heat map coloring pattern. When using make_otu_heatmap.py, higher relative abundance corresponds to more intense colors and low rel abundance uses lighter colors. However, apparently when relative abundance is zero, Qiime by default gives the DARKEST possible color from the color spectrum chosen. In other words, when using the default spectrum (YlGn) it's like this:
No hits (darkest green), lots of hits (dark green), few hits (light yellow). It would make a lot more sense if the otus not present in a sample were colored white or very light yellow. Is there a way to make this happen?
I've attached a heat map I made to illustrate this problem. In the last sample listed, "WS0a", the darkest color purple occurs for the otu represented by k__Archaea;p__Crenarchaeota;c__Thaumarchaeota;o__Nitrosocaldales;f__Nitrosocaldaceae;g__Candidatus Nitrosocaldus. However, as can be seen by the pie chart for this sample (also attached), this taxon does not occur in this sample. From the pie chart it is clear that the taxon that dominates this sample is k__Archaea;p__Crenarchaeota;c__MCG;o__pGrfC26;f__;g__, and this taxon is one of the darkest in this sample in the heat map, but not THE darkest. The lightest colored otu in this sample corresponds to k__Archaea;p__Crenarchaeota;c__MCG;o__B10;f__;g__, which is correct because there are hardly any hits for that otu in sample WS0a.
I should mention that the otu table I'm using has been filtered to a minimum count fraction of 1% for 11 different samples--maybe that has something to do with it?
While I'm at I'll bring up an only slightly related issue...the pdf file names generated for taxonomy charts are quite difficult to decipher. Is there a way to name them according to the sample name? Because of this it takes forever to find the right legend for each chart, I have to open the html file at the same time and then open each pdf legend file sequentially until I figure out which one is correct.
Thanks for the help and sorry if these have already been answered.