Alpha Rarefaction plots generated but not showing properly for categories other than Sample ID

[Rachel C.]

I have used the make_rarefaction_plots.py script to generate the plots for my data, and they look fine when I look at those for observed OTUS by Sample ID. However, when I sort by the category "defect" or "location", I get an odd-looking chart where the data is barely visible. To clarify, there are 91 samples, each of which is assigned one of three "locations" and one of six "defects." I validated my mapping file using the appropriate script so I do not think that is the source of the issue. Any insight would be appreciated. Thank you,

-Rachel

[Colin Brislawn]

Hello Rachel,

How many reads are in each of your samples? If memory serves, the rarefaction curve for a group of samples stops at the minimum read depth of those samples. So if a few of your samples failed to sequence, with only 10 or 20 reads, their curves would never make it on to this graph.

Let me know if that helps,

Colin Brislawn

[Muhammad Afiq]

Hi there, 

I have the problem where I cannot view the rarefaction plot. The details of each samples were there but I cannot view the image (plotted graph). When I saw your plot image, I think my browser kind of missing something which is the boxes besides each sampleID in the legend box. Mind sharing how? Thanks!

[Daniel McDonald]

Hi Muhammad,

Can you send a screenshot of what you do see?

Best,

Daniel