mothur

Graphs from Classity.otu tax.summary?

Can I use Classify.otu tax.summary tabular file to create graphs for my different samples?

I see that I have the real seq count in Classify.otu taxonomy but in it there are no samples. Then I see that in I have a tabular with the samples but the number there are somehow not representing the real count of sequences as in taxonomy? So can I use Classify.otu tax.summary for creating Krona or other charts, nevertheless it does not have the real sequences number bit another number that can be converted to a percentage?

Hi,

Sorry, I’m not a big fan of piecharts so, I’ve never had much use for krona plots. You can probably get what you want from combining the shared file and the cons.taxonomy files. For examples of how to do this with strip charts or bar plots, you might be interested in my minimialR materials.

Pat

I like krona plots for their instant gratification even though I agree with Pat on the pointlessness of pie charts as a final data viz technique. I subsample the *trim.contigs.good.unique.good.filter.precluster.pick.nr_v119.wang.pick.subsample.tax.summary (NOT the *.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.0.03.cons.tax.summary). I use Adam Caldwell’s script https://github.com/accaldwell/mothur_krona