R/MMPC.gee.output_script.R

In MXM: Feature Selection (Including Multiple Solutions) and Bayesian Networks

#class object for MMPC.gee output

#Class MMPC.gee.output

#MMPC.tempoutput object
# Function1: summary (generic for summary)
# Function2: plot (generic for plot)

#defining the class

setOldClass('proc_time')

setClass(Class='MMPC.gee.output', 
         slots=list(selectedVars='numeric', selectedVarsOrder='numeric', hashObject='list', pvalues='numeric', stats='numeric', univ='list', max_k='numeric', threshold='numeric', n.tests ='numeric', runtime='proc_time', test='character', correl='character', se='character'), 
         prototype=list(selectedVars=NULL, selectedVarsOrder=NULL, hashObject=NULL, pvalues=NULL, stats=NULL, univ=NULL, max_k=NULL, threshold=NULL, n.tests=NULL, runtime=NULL, test=NULL, correl=NULL, se=NULL));

setMethod("plot", signature(x="MMPC.gee.output"), 
          function(x,mode="all", ...){
            
            if(length(x@pvalues) <= 1000)  {
              mode="all";
            }
            
            if (mode=="partial")  {
              barplot(x@pvalues[1:500]);
              grid(nx = NA, ny = NULL, col = "black")
              b = barplot(add = TRUE,x@pvalues[1:500], main="Variables' Pvalues for null hypothesis: Ind(var, target)",xlab="Variable ID",ylab = "p-value" , beside=TRUE , border = FALSE)
              threshold_line = rep(x@threshold, 3*length(x@pvalues))
              lines(threshold_line, col="red" , lwd= 2.5)
              legend('topleft',  paste('threshold:',x@threshold, sep=" "), lwd= 2.5,col="red" , bty = "n")
              labels = c(1,x@selectedVars,length(x@pvalues))
              axis(1, at=b[c(1,x@selectedVars,length(x@pvalues))],labels=labels)
            } else {
              barplot(x@pvalues);
              grid(nx = NA, ny = NULL, col = "black")
              b = barplot(add = TRUE,x@pvalues, main="Variables' Pvalues for null hypothesis: Ind(var, target)",xlab="Variable ID",ylab = "p-value" , beside=TRUE , border = FALSE)
              threshold_line = rep(x@threshold, 3*length(x@pvalues))
              lines(threshold_line , col="red" , lwd= 2.5)
              legend('topleft' ,  paste('threshold:',x@threshold, sep=" ") , lwd= 3,col="red" , bty = "n")
              labels = c(1,x@selectedVars,length(x@pvalues))
              axis(1, at=b[c(1,x@selectedVars,length(x@pvalues))],labels=labels)
            }
          }
);