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tbj128 / mian

Mian is a platform for 16S rRNA OTU table visualization, data analysis, and feature selection
https://miandata.org
MIT License
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Probable future enhancement #6

Open ShailNair opened 3 years ago

ShailNair commented 3 years ago

Hi, Recently i tested Mian for my data. A few things which I think might be very helpful and if possible can be integrated into future versions:

  1. Regarding data processing: Currently, Mian has sub-sampling and lacks other filters like normalization, log transformation, rarefaction option.
  2. An important feature while visualization is filtering n number of top (down) taxa to make te visualization process more easy.
  3. More export options like vector image (svg,eps) or higher resolution scalar images would greatly enhance Mian.

Hope, this might be possible in future versions of Mian. Thanks for the great tool and all the hard work went into Mian.

tbj128 commented 3 years ago

Thanks Shail for your wonderful feedback! Apologies for the late response as I never had the notifications set up properly.

  1. Regarding the data processing, we currently don't support normalization and log transformation although I think those should be relatively easy to add in the future. Rarefaction (i.e. sampling equal number of observations from each sample) should be natively supported - we take the mothur terminology in that rarefaction = sub-sampling. Subsampling (removing samples is also supported). However, perhaps we could clarify this feature better!

  2. Filtering taxa is supported manually in the sidebar (i.e. filtering one or more) but you're right that we don't have support to choose n-top taxa. That's a great suggestion to incorporate in future releases.

  3. Exporting in PNG was actually chosen as it was believed to be easier for users to open. In fact, I think there's logic in the code to convert from SVG to PNG. That should be easy for us to add in the future. Thanks!