Heatmap with only genera data

Hi, I´m trying to build a heatmap from feature-table using taxonomy and metadata info. My issue is that I don´t know how to visualize only genera names in the heatmap (instead of all the taxonomic info. I´m using that script:

qiime taxa collapse --i-table 50filtered.qza --i-taxonomy taxonomy.qza --p-level 6 --o-collapsed-table table-filtered-top50-abundant-genera.qza

qiime feature-table heatmap --i-table table-filtered-top50-abundant-genera.qza --m-metadata-file metadata.tsv --m-metadata-column Atb-family --p-metric braycurtis --output-dir heatmap4

visualization.qzv (512.3 KB)

Thanks a lot!

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Hi @Manuss_Ponce,
Great question! Unfortunately, the answer is that there is no way to customize the names in QIIME 2 — easily.

You will need to export your taxonomy file, change the names to whatever you want, and re-import. Then collapse your feature table and build a heatmap using that taxonomy file.

Does that work for you? Sorry there’s not an easier way!

I will try that way. Thanks!

Hi, @ Manuss_Ponce,I am intersested to know how dealing with table.qza to generate 50filtered.qza . Can you share your indeas?

Hi Hupf!
What I did was to select the 50 features with higher median of relative frequencies (I don´t know if this approach is correct, I would accept some advise). I did it by hand in excel, exporting the feature table. Then, I built a metadata file with 2 colums: one with the OTU ids and another with the values TRUE or FALSE (the latter if each feature belongs to the top 50). Then I followed this:

qiime feature-table filter-features --i-table feature-table-1.qza --m-metadata-file METADATA.csv --p-where "Subject='FALSE'" --o-filtered-table 50filtered.qza

After that, I used collapse and so on.

I first built another heatmap using a table with the top 50 features in terms of total absolute abundance, but It doesn´t convince me, because of the associated bias. Maybe someone could provide another perspective, I,m quite neophyte in that field!!

I hope it helps you.

Thanks for your answer, I’ll try it .

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