Link to raw data behind figures

pending-development

#1

Hi QIIME2 developers!

I really like the way how data is represented in .qzv files for alpha and beta diversity analysis with direct links to download boxplots and statistical results as CSV files.
However, it would be also great to have a direct link to the raw data behind the plots (e.g. values of shannon diversity behind the plots showing results of shannon-group-significance). From my point of view this would be much more convenient than exporting the data from an archive .qza file.
In addition, I was wondering if it would be elaborate to change the PDF download option for beta distance boxplots into SVG as it is already for alpha diversity boxplots. This would make subsequent customizations of the boxplots much easier.

Thanks for your reply!


Acquiring the unifrac distance values shown in the beta group significance results?
(Matthew Ryan Dillon) #3

Hi @Mechah, thanks for writing!

Thanks, glad to hear!

Okay! We could make that happen, but first, what visualizations do you have in mind? Seems like alpha-group-significance is one of them, but maybe you are thinking of other visualizations as well? Once you respond with a concrete list of visualizations you have in mind, I will create support tickets on our issue tracker(s) (e.g. alpha-group-significance would get logged under q2-diversity's issue tracker). You are also welcome to create those tickets directly, but it is probably less work for you to just follow up here.

I completely agree! So much so that I actually already had an issue open to track this! The open issue is a bit open-ended, but I think adding SVG support would make sense there.

Thanks!


Raw data for alpha-diversity boxplots
#4

Thanks thermokarst!

Here is my list:
alpha_correlation: Alpha diversity correlation
alpha_group_significance: Alpha diversity comparisons
beta_correlation: Beta diversity correlation
beta_group_significance: Beta diversity group significance

Looking forward to see direct links from those visualizations (in SVG) to the raw data in an upcoming release of QIIME2.

Cheers!


(Drishti K) #6

This is on the same lines as the previous post, but is there a way to download the svg for the alpha diversity rarefaction plot. I’ve exported the underlying *.qzv and have access to the csv files, but I’m curious if there is a way to download the plot itself, instead having to take a snapshot of it. I can’t seem to locate the “Download SVG” functionality for the rarefaction plot.

Thanks,
Drish


(Nicholas Bokulich) #7

Thank you for the suggestion @drish_k! Adding this feature is already on our radar, but I do not have an eta for when that will be added. Thanks!


(Drishti K) #8

Awesome! thanks for letting me know, Nicholas!