I am new to R and randomForests so bear with me. I am trying to visualise my randomForest a little better using the MDSplot() function in Random Forest. There are two things i would like to do, and i dont know if they are possible or sensible.
1) Instead of just having colored markers on the MDSplot i want to have my sample names (row names) so i can see where each row falls, to see where each point clusters.
2) When i used my randomForest to predict on new data, i want to overlay them on the MDSplot (i.e. the PCA built from the proximity matrix which i trained my RF on) so that i can see how close the new data points lie next to the orginal clustered groups.
Thanks for your help, Anthony
P.s if you have any other suggestions on how to visualise the RF those are great too!