Gallery does not load

[Noriko Okamoto]

Hello there,

I'm trying to use Phinch to visualize the taxonomy table that I got from my colleague. The original file was a tablineated text, so I converted to biom and added metadata following the instruction at 'help' tab. The data seems to load, as the 'filter data' page is shown properly. But when I "proceed to gallery" and pick up a chart, it does not show. Is it because a too big a file size, or other issues?

Thanks,

Noriko

[Holly Bik]

Hi Noriko, can you answer a few questions for me:

How big is your .biom file? 

Are you accessing http://phinch.org in the Google Chrome browser?

I'm assuming by "taxonomy table" you mean an OTU table from QIIME?

If the metadata is loading in the first parser window, then the file should be working OK. Sometime the visualization gallery is slow to load with big .biom files (>100MB); we haven't optimized loading time for super large files yet. I've also noticed that if you have a lot of samples, and some metadata values are unique for each sample, this can really slow down the gallery loading (for example, if you have altitude data where no two samples are likely to have the same value). We're still in the prototyping phase so we haven't optimized for this scenario yet either, but it would be good to narrow down the potential issues with your file loading.

[Victoria Byrd]

I am having this same issue. My file is a 0.6 MB json-formatted biom file, created by using the biom add-metadata command to add metadata to an OTU table. No metadata values are unique for each sample, so that couldn't be the issue. The gallery has just been loading and loading all weekend so I'm fairly certain there is some issue with the file but can't figure out what it is. Any help would be appreciated, thanks!

[Holly Bik]

Hi Victoria,

I would suggest trying to regenerate the OTU table from scratch in QIIME (following Step 2 on this page, starting with make_otu_table.py https://github.com/PitchInteractiveInc/Phinch/wiki/Quick-Start). 

Or else you could try back converting to classic and re-converting the JSON, following these instructions: https://groups.google.com/forum/#!topic/phinch/rsIk8DCQ0VM

Some people have had occasionally had problems with BIOM tables coming out of QIIME 1.9 (and we've never been able to figure out why), so if that is the version you are using you could also try going back to QIIME 1.8 and redoing the same commands. As always, make sure your JSON file is BIOM 1.0 formatted (look in the header).

Hope this helps,

Holly

[Victoria Byrd]

Thank you Holly, I actually got my initial OTU table--the one that didn't work--from a different pipeline my lab is testing (one that is still in the development phase) and not from QIIME, so that may have been the issue. I realized that as a result of using this pipeline, my OTU IDs were not numbers, but instead contained taxonomic information--perhaps that was the problem? Regenerating the OTU table from scratch using QIIME (1.9) worked perfectly, either way. 

Thanks again,

Victoria

[Jumria Sutra]

Hi, i know this has been a long time but i need help as my phinch also wont load the galery. My biom file is only 0.3mb, has the 1.0format but it still wont load the galery. can you help me on this ?