abundance figure

[lsbrueck]

"Right now we are working only through the 16S - a cool figure would be like the one you did for the L4 6 year paper but for each biome - would be great to show the abundance for each taxon in such a tree - this is one suggestion" cite from Jack

Basically you want an abundance graph for each data set, or one figure with pie charts for each node showing the proportion in each data set?

[gilbertjack]

That sounds interesting - or how about an abundance and persistance tree - like in the ISME paper showing the abundance of OTUs as circle size and their ubiquity as a colour gradient - so we see if the most abundant OTUs are also the most shared between biomes?

[lsbrueck]

Okay, I had a look on the different files. However, I'm a little bit confused. I cannot find files in which the label for the different OUTs are specified. Is there a list like in the last project specifying OTU ID and label (place in the taxonomy). Or am I completely misunderstanding something here?

[gregcaporaso]

What information would you need exactly? I don't think there is any data
that exists right now that exactly matches what you're looking for.

On Fri, Aug 17, 2012 at 6:58 AM, lsbrueck [email protected] wrote:

Okay, I had a look on the different files. However, I'm a little bit
confused. I cannot find files in which the label for the different OUTs are
specified. Is there a list like in the last project specifying OTU ID,
abundance and label (place in the taxonomy). Or am I completely
misunderstanding something here?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/31#issuecomment-7818508.

[lsbrueck]

To produce a graph with abundances like in the L4 project I need some information regarding the label of the different OTUs. For instance the position in the taxonomy of life, something that represents the tree structure.

[gregcaporaso]

this will be dependent on issues #26 and #27, which aren't ready right now, but should be ready this week.

[rob-knight]

What would be useful here is plots per-biome that have on the x axis the number of samples (or perhaps the fraction of samples) and on the y axis the # OTUs that are in that # of samples -- not sure if this will be better as separate graphs or if as one graph colored by biome type.