Filtering Results of taxa plot and heatmap

(Clinton) #1


I am conducting a meta-analysis of several studies so when I run the following codes I get huge plots.

qiime taxa barplot
–i-table table.qza
–i-taxonomy taxonomy.qza
–m-metadata-file sample-metadata.tsv
–o-visualization taxa-bar-plots.qzv

qiime gneiss dendrogram-heatmap
–i-table table.qza
–i-tree hierarchy.qza
–m-metadata-file sample-metadata.tsv
–m-metadata-column Subject
–p-color-map seismic
–o-visualization heatmap.qzv

I understand that I can filter the tables using “qiime taxa filter”, but I was wondering if there was a way to filter the results to include the top 50-100 hits based on the metadata file/column provided.

Thank you for any help.

(Nicholas Bokulich) #2

What do you mean by “top 50-100 hits”? Do you mean the 100 most abundant taxa or something along those lines?

See qiime feature-table filter-features. This will allow you to filter features either based on abundance or based on a list of features you want to select or exclude, or based on some feature metadata.

(Clinton) #3

Specifically for the heat map, I want to “zoom in” on the top features to see what might be causing them to be different.

Honestly, I need to cut down the number of reads, but I don’t really know how to do it. Just running the top 100 taxa probably would help a lot. I will try to figure out how to do that.

Another thing, I thought might be a good idea was to combine reads that are all from the same metadata category. Is this something I can do? And is it advised?

Thank you again for your help. I apologize for my lack of description and comprehension.


(Nicholas Bokulich) #4

Use qiime feature-table filter-features, setting the min frequency at an appropriate level.

Do you mean group samples that share the same sample metadata value? See qiime feature-table group. Definitely not a bad idea when making heatmaps if you have many groups…

Let us know if that scratches your itch! :mosquito:

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