Download All Kruskal-Wallis Results


(Zach Burcham) #1

Hello,

I have a lot of metadata factors and was wondering if there is a simpler way of viewing all the results from the Kruskal-Wallis testing. For example, I ran a pairwise Kruskal-Wallis analysis of the Observed OTUs and want to be able to just download all the H-vals, p-vals, etc. for all metadata columns without having to use the drop down box to go to each and download individually. Is this possible?

Thanks,
Zach


(Nicholas Bokulich) #2

Alas there is not a QIIME 2 command to export these as a fancy table, but doing so should be fairly easy using qiime tools export.

qiime tools export \
  --input-path observed_otus-alpha-significance.qzv \
  --output-path observed_otus-alpha-significance/

This will create a directory containing a whole bunch of different data files. If you want the per-column kruskal-wallis results, these are stored in a bunch of JSON files that you should be able to parse easily enough, and the within-column pairwise group comparisons are stored in a bunch of TSV files sharing the filepath observed_otus-alpha-significance/kruskal-wallis-pairwise-*.

I have nothing on-hand but if you or another forum user work out a quick script to parse these data to generate a nice table, please do share here!


(Zach Burcham) #3

Thanks for response @Nicholas_Bokulich. I exported the JSON files and it seems they are in JSONP format. Is there an easy way to convert JSONP to JSON so it can be parsed?


(Matthew Ryan Dillon) assigned thermokarst #4

(Matthew Ryan Dillon) #5

Hey there @Zach_Burcham! JSONP is just JSON, just pull the arguments out of the function (or, write your own function to be called by the padding function).


(Matthew Ryan Dillon) unassigned thermokarst #6

(Zach Burcham) #7

Hi @thermokarst, one more question. Can I do something similar for the beta diversity group significance? I unzipped one of .qzv files from beta-group-significance and there are no JSONP files for this one. I can find the pvalue for the overall model in the HTML file, but is that the only place it is saved?


(Matthew Ryan Dillon) assigned thermokarst #8

(Matthew Ryan Dillon) #9

Unfortunately not - that viz isn’t dynamic like the alpha-group-significance viz. Sorry! :qiime2: :t_rex:


(Matthew Ryan Dillon) unassigned thermokarst #10

(system) closed #11

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