generalized read and plot.xvg

[jspaezp]

Hello, I attempted to modify the treatment of the .xvg files implementing

• generalization of the read.xvg function to deal with cases where time is not the x axis
• added a .xvg file where that is the case (radial distribution function)
• changed the structure of read.xvg by using internal functions
• changed the output of read.xvg from a matrix to a data frame (subject to discussion)
• reorganized plot.xvg to make use of read.xvg
• made plot.xvg restore the par configuration after running
• modified plot.xvg to plot maximum 4 facets per row (instead of all plots in a single row)
• removing the addition of plot.xvg as a method (since there is technically no class xvg that is being implemented)
• added plyr as a dependency due to the use of ldply in plot.xvg (subject to discussion, the same result could be done by using sapply > t > as.data.frame)

Let me know if those are found to be useful of if any modification should be done.

[dosorio]

Hi Juan, I am agree with the generalization of the x axis for the read.xvg function (I already made the change in the develop branch some days ago) All others changes are very useful! Thank you so much! However, I try to maintain the Peptides package without dependencies. Would you change the code to don't use plyr as a dependency?

[jspaezp]

Done In addition i was wondering whether it would be useful to add a statement that tests whether the provided file is actually an xvg file ... let me know if you have any insights about it. Best

[dosorio]

Thanks for the changes! They will be added in the next version of Peptides. About the XVG format standard, I know that GromacsWrapper implementation (Python based) has a full function to validate and read xvg files. You can check it at: http://pydoc.net/Python/GromacsWrapper/0.3.2/gromacs.fileformats.xvg/