Alpha rarefaction non-categorical data

General Discussion
1

Hi i’m new to qiime and currently going through the Parkinson’s mouse tutorial - i’ve generated an alpha rarefaction plot of the data - however it states that one column (days post transplant) could not be included in the rarefaction plot because it doesn’t contain categorical data

why is it that non-categorical data cannot be analysed / contained in an alpha rarefaction plot?

Appreciate any suggestions - thanks!

3

Hi!
You still can perform the analysis by adding a new column in your metadata and adding to numerical data categorical
For exmaple

Old column....New column
14 ...........14_dpt
7 ............7_dpt
21............21_dpt
4

ahh thank you for this! - worked nicely

6

Imagine if your non-categorical data had values in the range of 1-100. If this was treated the same as categorical data, the "column" drop down menu in your visualization would include 100 extra options. Do you see why that wouldn't be very useful? The reason the solution above works is because the values in New column are inferred to be categorical since they are strings rather than integers.

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7

Great explanation - thank you!

8

see also this tutorial for a way to tell QIIME 2 whether you want a metadata column to be interpreted as numeric, categorical, or both: https://docs.qiime2.org/2020.2/tutorials/metadata/#column-types

No need to make a new column to force QIIME 2 to interpret as categorical.

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