I want to build a Heatmap from my feature table, but I only want to select those taxa with differential abundance according to Lefse (in this case). The problem is that I need to keep up some genera, some families, orders, etc. I know how to filter some genera and how to collapse the filtered table to genera, but I don´t know how to select and combine taxa from different categories.
Maybe I don´t explain it properly
The most straight-forward way to do this would probably be to filter your table by feature ID. You can use
feature-table filter-features with some feature-metadata (same rules as sample metadata, the IDs are just referring to features instead of samples) to accomplish that.
So, what would that look like code wise? IF you had like Staphlococcus, Lactobacillus, and Pseudomonas (example, short of course), and you only wanted that heat map, how would you narrow that down? I keep trying to do something similar (PcOA with only one or two significant species) and it just keeps failing.
It depends on if you have the feature-ids already, in which case the above command is basically all you need. But if you are trying to filter by taxonomy specifically, then you should use qiime taxa filter-table which will filter based on an additional FeatureData[Taxonomy] artifact.
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