Thanks to the help I've received on the forums, I have completed my first QIIME2 workflow and produced a number of barplots, PCoAs, etc from the analysis. I am interested in publishing some barplots of order-level taxa for each group of samples, but there are many low-frequency taxa that are invisible on the plots but taking up lots of space on the legend. I'd like to merge taxa below a set relative frequency threshold (2% but maybe more) into an "other" category to clean up the visualization. Is there a way to do this in QIIME2? Thanks for the help!
Hello! I do not think that you can achieve this goal using Qiime2 standard tools (please, correct me if I am wrong). But here are some alternatives:
- Use Qiime2 generated barplot as it is and modify a legend (just cut it) and explain in the figure description that legend represent only top N taxa.
- In the barplot, if you will click on the color box in legend, it will show you only this taxa on the barplot. You can just click on the top N taxa in the legend, and everything else will be without color. Use this image and cut the legend correspondingly.
- Modify barplot and legend as svg files in any svg editor.
- Download taxa counts from the barplot as csv and plot it using R or Python.
Hi Timur, thanks for the reply. Some of the taxa are invisible in the group but when I click on them in the bar legend in QIIME2 view I see faint lines appear, so it might be hard to physically cut the graph. I think I may try to do this in R or Python, or even download the values into Prism to make easy stacked bar graphs and then I can just sum the remaining taxa into a 2% category that way.
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