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