mothur

rarePlot in R ??

Hi everyone,

I m trying to use some files created in mothur (outfile from the command rarefaction.single) in R.

I found the package mothuR but this is not possible to install it on recent R version. Then I just unzip the function rarePlot copy/paste in R studio click enter to run it. No problems poped up but the help (https://github.com/SchlossLab/mothuR/blob/master/man/RarePlot.Rd) is not enough for me and I would like to get more details.

\item{file}{
The .group.rarefaction file which you wish to plot. Only works for the output of rarefaction.single from mothur. What kind of stuff we have to place before and after the file name : we can use / or \ ? and ’ or " ? C:/users…rarefaction or we have to place the data in Rstudio before ?

\item{groups}{
The specific groups within x which you wish to plot, in list form c(“Examplegroup1”, "Examplegroup2’). either the names ie c(“m24626d36”, “Day3”) or the number the group falls in the list of all groups. ie c(1,4,7) (the 1st 4th and 7th group). Do we just have to write (file,c(1,2,3,4,5,6),ylab…) for the groups item or we have to place ’ or " just when there is a specific name in it ?


and then what do we have to write exactly to get graphs please, because I m lost

Thank you very much in advance for all of you,

Have a nice day,

best regards,

nicolasc

What are you trying to do? I haven’t played with mothuR but may be able to suggest ways to do whatever it is you want in other packages.