Hi there,
I am new to QIIME2 . I made the heat map and propotion plot but I had hard time in Interpreting results. Is there any way we can insert phulum or any level in the heat map?
Absolutely. Use qiime taxa collapse at different levels (e.g., phylum). Then use that feature table as input to heatmap.
Good luck!
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HI Nicholas,
Thank you so much. Do you have any example script for this qiime taxa collapse?
your help will be highly appreciated.
from the moving-pictures tutorial:
collapse at genus level:
qiime taxa collapse \
--i-table gut-table.qza \
--i-taxonomy taxonomy.qza \
--p-level 6 \
--o-collapsed-table gut-table-l6.qza
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Nicholas, Thank you so much. I can generate collapse table using your script, but when I tried to generate heat map , I got this error. It would be great if you can take a look and help me to fix it.
Thanks a lot.
oh I see — you are not using qiime feature-table heatmap, you are using q2-gneiss.
Did you see the gneiss tutorial? The directions are all in there (use a collapsed table in the same way).
Good luck!
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Yes, I read Gneiss tutorial and ran the script and I got this image.
Now, my concern is how to interpret this result, and I know this is differential abundance but how can I label this heatmap with the respective genus. I didn't see any information regarding this in gneiss tutorial.
Thanks.
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Looks like qiime gneiss dendrogram-heatmap cannot be labeled by taxonomy. Looks like qiime gneiss balance-taxonomy is the appropriate follow-up method to examine taxonomic differences between groups.
For example, you can look at balance y0 to see which features (labeled by taxonomy) are associated with that balance (which seems to differentiate one of the “fast” samples from all other samples — in general it looks like there is more subject heterogeneity among your samples than there are group differences, so drawing conclusions may be difficult)
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