[R] Ask help

[Jim Lemon]

On 04/04/2013 01:31 AM, DONG Echo wrote:
> Hello!
>   I am eager to learn if I only have a data about the relationship between otu and sample, could I use the function capscale, and final make a point plot that x-axis is CAP1 and y-axis is CAP2?   Besides, what function could I use to make the different rarefaction curve with different color in the a plot in R? Appreciate very much.
>                                                                                                                                           Sincerely!
Hi Echo,
This is such a great question that I am going to try to answer part of 
it. OTU tables are roughly observation by category tables, and as you 
mention the capscale (vegan) function, this will probably reduce to 
sampling unit by species. The CAPx scores can be plotted on 2D 
coordinates as in the first example from the capscale function. However, 
it does not seem to make any sense to overlay rarefaction curves on the 
CAP plot as the two are completely different measures. Displaying the 
two plots side by side would probably be a better idea.

I tried to answer this for four reasons:

1) I didn't see another answer.
2) I thought it might be fun to find out what an OTU table was.
3) The question is an archetype of asking something highly specific 
without providing the necessary information for anyone but the 
questioner to understand it.
4) It struck me that the reverse often occurs, with answerers providing 
information that the questioner has little chance of understanding 
without a substantial amount of introduction.

Jim