Too many samples to show on taxa bar plot

[1115 (Jonathan Yoou)]

Hi to all.

I’m analyzing a project and I get a result what I need, a taxa bar plot file.

But view.qiime2.org can’t show the plots with it. I guess that’s because samples on it are too many… over 400.
Is there a way to see the result?? I think

1. Analyze with groups from the first step, like sampled location or specific treatment. But it takes some time to do from the beginning so I think this is the last option

2. Collapse features to level 7 so that I can get only the information what I need for my analysis. I don’t try it yet since all of cores are being used now. I think this is the most reasonable option for me…

Is there another option to do? Or if my options I suggest are wrong, could you tell me which that is?

And this is a little bit off-subject, some of my samples of another project in taxa bar plot show only class level classification. I used SILVA full length pre-trained classifier. Do I have to train my own classifier for these samples? How I understand about SILVA full length pre-trained classifier is that it is trained with ALL taxonomy and rep-seqs(16S, 18S ,ITS) not limited on V4, but whole length of them. That’s why I chose to use it even though it is time-consuming…
If there is no problem what I did, then is it a problem of my samples sequence quality??

Thank you!

[Nicholas_Bokulich]

@1115

But view.qiime2.org can’t show the plots with it

What error are you getting? Or what do you mean by can't show the plots? It may just be taking a very very long time to load. 400 samples is not too many at all, though an enormous number of taxa could be the issue.

1. does the plot load at all or does it just fail to reload when you choose a deeper taxonomic level?
2. what browser are you using?

I'm trying to figure out if it is actually failing to load or just taking a really long time, and if there is an error if it is related to your browser. Sharing your qzv file could help us troubleshoot.

@1115

1. Collapse features to level 7 so that I can get only the information what I need for my analysis. I don’t try it yet since all of cores are being used now. I think this is the most reasonable option for me…

This will not work for plotting a barplot. You could use a collapsed table to make a heatmap.

@1115

And this is a little bit off-subject, some of my samples of another project in taxa bar plot show only class level classification.

That is very off-topic. Please open a separate topic for this question.

Thanks!