Moved to Processing Implementations...
You might use Ajax to send the data to the server. Not sure if there is something more PJS built in.

Thanks, I worked it out. It ended up being alittle more complicated than I expected. Basically what I had to do was create a php script which writes its url arguments to a file, then on my processing.js page created a javascript method as per below which called that php script. Then from my processing code called the javascript method sendData() which I had written:

For short amount of text (fitting in the parameters of an URL), one can use, in classical Processing, loadStrings with an URL to transmit these parameters. If loadStrings works this way in PJS too, it can be simpler for you...
I suggested Ajax because I didn't know the size of the data you needed to transmit.

you can use loadStrings() in pjs to get content from a text file in but browser restrictions prevent directly writing files to the system. you have to use a work around method with server side code like the above example mentioned.

post to a php script or create a web service of some kind to send your data off to with JavaScript.