taxa-bar-plot visualization

Hi All,

QIIME2 generated a taxa-bar-plot.qzv for data visualization in qiime2 view. While this bar plot is nice and powerful, I don’t think it is publishable in its current format. The bars are long and narrow, some times I would need to scroll down to see the whole image or to match the taxon names and the bars. My question is:

  1. is there any way to customize the taxa-bar-plot in qiime2 to be publishable?
  2. if other software or tools are needed for this purpose, could you please let me know the common ones?
  3. if I want to use R to visualize the taxa-bar-plot, could you please recommend some common ones?

Thank you very much in advance!

Hi @arlandan,

You definitely have some options! Have you played around with the vega editor button in hte qzv? I think this should give you more control over your figures. Alternatively, a lot of people will export their data as a tsv, and as you suggest, take it over to their favorite plotting software. I dont think there are clear recommendations here: excel, graph pad, seaborn, ggplot, a really good ruler and pen… whatever works best for you. If you’d like to import into R, though, I’d suggest looking into the qiime2R library.


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Hi @jwdebelius,

Thank you very much for your help. I was not able to find the vega button in qiime2 view when visualizing my qzv file. I googled it and looks like I need to install vega/editor something like that. But it said it needs yarn installed first. Then I am lost from there, since yarn needs something else preinstalled first… … and th installation is not working as expected, since there is alway some package is missing. I am having a hard time figuring this out :frowning:

When the yarn installed, “yard start” command not working. I know this is a bit away from qiime2 discussion, but I am just stuck in there and could not move forward. Am I on the right track? Thank you!

All the best.

Hey @arlandan, unfortunately this viz isn’t built on vega, so installing vega isn’t going to help out much. Your best option is to look at the “export” options @jwdebelius provided above.

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Thank you very much @thermokarst @jwdebelius for your suggestions. I would go with exporting and visualization in R.

All the best.