search

PhinchApp / Phinch

Phinch is a data visualization framework aimed at promoting novel explorations of large biological datasets (microbiomes, metagenomes, etc.). Features include support for HDF5 and JSON BIOM files, retooled visualizations, improved image export and sharing, and the ability to work offline.
BSD 2-Clause "Simplified" License
36 stars 9 forks source link

Visualisation only showing Phyla level and not class, order, family, genus, etc #11

Closed dhuyben closed 1 year ago

dhuyben commented 5 years ago

I made a biom file from 16S OTU data in Mothur using the Silva database. The file imports fine, but when I visualise the data, it only shows the Phyla level and there is not button to select the other levels (eg Order).

Is there a problem since I used the Silva instead of Greengenes database? I see that the taxonomy levels are in quotations instead of underscore and I wonder if that is a problem. I don't code in QIIME and I can find any help using Mothur. Any help would be great! Below is the first few lines:

"id":"stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.shared-0.03", "format": "Biological Observation Matrix 0.9.1", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "mothur1.42.3", "date": "Thu Jul 11 13:56:44 2019", "rows":[ {"id":"Otu00001", "metadata":{"taxonomy":["Bacteria", "Firmicutes", "Bacilli", "Bacillales", "Bacillales_unclassified", "Bacillales_unclassified"], "bootstrap":[100, 100, 100, 100, 97, 97]}},

vebaev commented 5 years ago

Same thing here, showing only 1 level and the level drop-down menu is missing. (the biom is from mothur)

mikeschhorn commented 4 years ago

Same thing here - however, import of same mothur biome files that don't work in the new app into the old phinch web-app (https://usegalaxy.eu/phinch/viz.html) show full taxonomy - but there generating images stalles and no option for grouped taxonomy barcharts.....

Piplopp commented 4 years ago

Hi, I have the exact same issue and I poked around a bit, the issue of not having the dropdown seems to be because we are missing the prefixes like k__ before each level.

After adding the same prefixes as the GreenGenes database (k__, p__, c__, o__...) I get the taxonomy bar back. If I add arbitrary prefix levels I get all the arbitrary levels just as expected.

If there is no prefixes however it still only shows the first level.

Zubyluche commented 2 years ago

Hi dhuyben,

how did you get your mothur converted Biom file to upload perfectly on Phinch?. When I upload my mothur converted biom file, it throw an error "the file uploaded doesn't validate for phinch". Please, I will need some direction or pointers here.

Thank you

dhuyben commented 2 years ago

Hi Zubyluche, I did this a long time ago and I am not an expert. I imagine you did not make the biom file correctly. Maybe you are missing a shared, meta, constaxonomy or other file. Here is the code I used: make.biom(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.shared, metadata=stability.meta, constaxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.cons.taxonomy)

When you open the biom file as text it should look like my first post. You can also find more info here: https://mothur.org/wiki/make.biom/

Zubyluche commented 2 years ago

Thank you so much dhuyben. I appreciate your response . I succeeded in uploading the biom file on phinch but I realized that phinch app doesn't make different graphs except the bar stacked graph.

On Tue, Jan 4, 2022 at 1:45 PM dhuyben @.***> wrote:

Hi Zubyluche, I did this a long time ago and I am not an expert. I imagine you did not make the biom file correctly. Maybe you are missing a shared, meta, constaxonomy or other file. Here is the code I used: make.biom(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.shared, metadata=stability.meta, constaxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.cons.taxonomy)

When you open the biom file as text it should look like my first post. You can also find more info here: https://mothur.org/wiki/make.biom/

— Reply to this email directly, view it on GitHub https://github.com/PhinchApp/Phinch/issues/11#issuecomment-1005078236, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMQITWNMTMHTT4MGW2IK26LUUM545ANCNFSM4IDVAEAQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you commented.Message ID: @.***>