is it possible to generate a heatmap using the classify info

Commands in mothur
1

I’m wondering if it is possible to generate a heatmap from e.g. the taxonomy string generated after running classify.seqs, somehow.
e.g. is there a way to generate a heatmap that considers everything at a particular taxonomic level as one grouping (e.g. the order level, or family, phyla etc etc)
This is for when you don’t know exactly what cluster level (e.g. 0.03, 0.05, 0.10) corresponds to family/order/phyla etc

Thanks

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This type of data would be in the summary file that comes out of classify.seqs

3

Thanks for the reply.
Could you please give me a little more information?
e.g. how can I tell from the summary file (after running classify.seqs) what OTU clustering level corresponds to genera, which to family, which to phyla across my dataset?
i.e. if I want to run heatmap.sim(shared=filename.shared, label = XX corresponding to phyla level clustering…)

Or is it possible to run heatmap.sim(shared=filename.shared, label = link to the summary file somehow)?

Thanks for you help and your patience,

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level 6 from the phylotype command corresponds to phylum - if you are using the RDP or recent SILVA reference files. It is 7 if you are using the greengenes reference.

5

Thanks for the reply.
I understand the classify file, just not how to determine the OTU clustering level that corresponds to each level in that classify file.
Because as far as I can tell, I need the OTU level to use the label command with the heatmap.sim command (?)

e.g. I can make a heatmap at OTU level 0.03, 0.04, 0.05, 0.10 etc etc etc using the label function with the heatmap command.
But, which one of these OTU levels corresponds to e.g. phyla or e.g. genera

i.e. a reviewer has asked to see a heatmap at family level and also at phylum level and I can’t determine how exactly to run heatmap.sim to generate that for him/her…
Thanks again

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e.g. I can make a heatmap at OTU level 0.03, 0.04, 0.05, 0.10 etc etc etc using the label function with the heatmap command.
But, which one of these OTU levels corresponds to e.g. phyla or e.g. genera

This simply is not possible. 0.03 generally corresponds to something below the level of a genus, but the other levels are so uneven that it is impossible to assign a taxonomic level to a distance-based cutoff. If you want a heat map at a specific taxonomic level, you will need to run phylotype and then make.shared on the output and use the appropriate taxonomic level.

Pat

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Thanks Pat.

Cheers,
Emma

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Hi,
I also want to create the heatmap.bin in which OTUs is assigned to phylotype. I used phylotype, made a shared file, then I made the heatmap.bin. But the heatmap.bin not include which OTUs correspond to phyla or genera?
Please help me1
Thank you very much