I applied pairwise Kruskal - Wallis on alpha diversity indices for my treatments. I got box plots and can deduct the result from the box plot that the alpha diversity in T1 is higher/lower than control. However, I could not get any box plots for beta-diversity, that I may say that beta diversity is higher or lower in T1 than control? I have applied non-parametric permanova and anoism however they just give me a p and q value, which just showed significant differences or no difference. Can anyone help me on this? I want to make box plots that beta diversity in the T1 is higher or lower than control.
Please check out the Alpha and Beta significance section of the moving pictures tutorial again, and try the --p-pairwise flag on your qiime beta group-significance to get boxplots.
However, it’s worth noting that beta diversity doesn’t function the same way as alpha diversity, since we’re looking at distances (difference) between samples. This has a couple of implications. First, it means that you’re always looking at your data as an intersection between two parameters. Your boxplots are of the distance between group A and itself (within A), group B and itself (within B) and between A and B (a vs b).
We have to make a comparison across the groups, because we can’t develop an innate sense of magnitude. (And sometimes magnitude is contextual anyway.) For instance, if I say something is 2 away, it’s hard to tell what the distance actually is without units. Two could be 2 hours, 2 minutes, 2 leagues, 2 blocks, 2 feet. I And whether that’s “near” or “far” depends on those units. Unfortunately, distances in microbial ecology don’t have easy to use units, so we can’t use that as a measure of “near” and “far” (similar and disimilar). But, if you know the distance from X to Y is 2 and the distance from X to Z is 8, then you know that X is closer to Y than it is to Z.
So, when you’re doing your statistical test, you’re essentially asking if theres a difference in distances within group A or within group B or between A and B. Looking at the boxplots can help you judge if that difference is because there’s a larger within-group distance, or because the between group distance is larger than the within group distance. Each of these, in turn, have different implications for your interpretation…