I have some 3D PCoA from qiime emperor plot command. I uploaded it to qiime viewer website. It looks good overall. However, if I want to have a higher resolution of the 3D PCoA, especially the light effects of the balls. I cannot find a way to do it. I googled a bit and I think three.js is the shape rendering engine behind emperor, is there a way to quickly change the setups in emperor to allow a much higher resolution for publication purposes? Thanks. Jianshu
Hi @jianshu93,
Have you looked at the two Save Image options? You can access these by clicking the gear icon toward the top-right of the ordination plot, as illustrated here:
If that doesn’t get you what you need, you might also be interested in the qiime vizard scatterplot-2d action, which generates arbitrary scatter plots from QIIME 2 Artifacts and metadata. For example, if you have the unweighted unifrac pcoa QZA file from the Moving Pictures tutorial, and the sample metadata, you could generate one of these as follows:
qiime vizard scatterplot-2d \
--m-metadata-file unweighted_unifrac_pcoa_results.qza \
--m-metadata-file sample-metadata.tsv \
--o-visualization uu-scatterplot.qzv
(Example output from that command: uu-scatterplot.qzv.)
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Hi @gregcaporaso , yes I did but the 3D effect was lost after saving to SVG/PNG (the ball is a strange 2D in a 3D system after saving). I do want a 3D with the effect, which is more informative in my case (and very cool). –Jianshu
Ok, makes sense @jianshu93. I'm not sure that it's possible to retain that effect when exporting. @yoshiki, do you have any ideas?
should be ok if the effect is only in the view mode. I can do high resolution screenshot. But the resolution is not high enough in the view mode now.
Unfortunately there’s no workaround for this. SVG exports have always been a bit quirky with the underlying rendering engine.
I appreciate your patience with my slow reply!
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