just use RMSE

Just use RMSE since some time it could oppositive results with Q values

Author: guokai8

R/o2plscv.R

@@ -72,20 +72,20 @@ o2cv<-function(X, Y, nc, nx, ny, group=NULL, nr_folds = 5, ncores=1,
     res <- do.call("c",res)
     results <- as.data.frame(t(sapply(res, function(x)unlist(x))))
     results <- results%>%group_by(nc,nx,ny)%>%
-        summarise(Qx=mean(Qx),Qy=mean(Qy),Px=mean(Px),Py=mean(Py),Rx=mean(Rx),Ry=mean(Ry))%>%
-        mutate(RMSE=Rx+Ry,Qxy=sqrt(Qx^2+Qy^2))%>%arrange(desc(Qxy))
+        summarise(Px=mean(Px),Py=mean(Py),Rx=mean(Rx),Ry=mean(Ry))%>%
+        mutate(RMSE=Rx+Ry)%>%arrange(RMSE)
 
   ### results <- results%>%filter(Qx>=0,Qy>=0) 
    ### not sure if meaningful                                   
     nc <- as.data.frame(results)[1,1]
     nx <- as.data.frame(results)[1,2]
     ny <- as.data.frame(results)[1,3]
-    Qxy <- as.data.frame(results)[1,11]
-    RMSE <- as.data.frame(results)[1,10]
+  #  Qxy <- as.data.frame(results)[1,11]
+    RMSE <- as.data.frame(results)[1,8]
     message("#####################################")
     message("The best parameters are nc = ",nc,", nx = ",nx,", ny = ",ny)
     message("#####################################")
-    message("The Qxy is ",Qxy, " and the RMSE is: ", RMSE)
+    message("The the RMSE is: ", RMSE)
     message("#####################################")
     return(results)
 }
@@ -163,9 +163,11 @@ o2cv<-function(X, Y, nc, nx, ny, group=NULL, nr_folds = 5, ncores=1,
         # Restore to original values
         Xev <- X[cls.grp == k & is.na(cls.grp)==FALSE,]
         Yev <- Y[cls.grp == k & is.na(cls.grp)==FALSE,]
-        
-        tmp <- list(k=k, nc=n, nx=nx, ny=ny, Qx=abs(Q(Xev,X_hat)),
-                    Qy=abs(Q(Yev,Y_hat)),Px=s2(Xev-X_hat),Py=s2(Yev-Y_hat),
+        #####
+        #### just use the RMSE to determine the best paramaters
+        ### some thing shown wrong results with Q values
+        tmp <- list(k=k, nc=n, nx=nx, ny=ny, 
+                    Px=s2(Xev-X_hat),Py=s2(Yev-Y_hat),
                     Rx=rcpp_rmse(Xev,X_hat),Ry=rcpp_rmse(Yev,Y_hat))
         results <- append(results, list(tmp))
     }

R/plot.R

@@ -149,7 +149,6 @@ plot.O2pls <- function(x, type = "score", var = "Xjoint",group = NULL,
 #' @importFrom stats reorder
 #' @param x an o2plsda object
 #' @param type score, vip or loading 
-#' @param var specify Xjoint
 #' @param group color used for score plot
 #' @param ind which components to be used for score plot or loading plot
 #' @param color color used for score or loading plot
@@ -172,14 +171,19 @@ plot.O2pls <- function(x, type = "score", var = "Xjoint",group = NULL,
 #' plot(fit0, type="score", group = factor(yy))
 #' @export
 #' @author Kai Guo
-plot.o2plsda <- function(x,type = "score", var = "Xjoint",group = NULL, 
+plot.o2plsda <- function(x,type = "score",group = NULL, 
                         ind = c(1,2), color = NULL,
                         top = 20, ellipse = TRUE,order=FALSE,
                         pt.size = 3, label = TRUE, label.size = 4,
                         repel=FALSE, rotation =FALSE,...){
     if(type == "score"){
         dd <- scores(x)
-        va <- x$xvar[2,ind]
+        if(x$ncomp==1){
+            va <- x$xvar[2,1] 
+        }else{
+            va <- x$xvar[2,ind]
+        }
+        
         dd <- as.data.frame(dd)
         if(ncol(dd)==1){
             dd <- dd[, 1, drop = FALSE]
@@ -216,8 +220,12 @@ plot.o2plsda <- function(x,type = "score", var = "Xjoint",group = NULL,
         if(isTRUE(ellipse)&!is.null(group)){
             p <- p + stat_ellipse()
         }
+        if(ncol(dd)==1){
+            p <- p + xlab(paste0("LV",ind[1],"(",round(va[1]*100,2),"%)"))
+        }else{
         p <- p + xlab(paste0("LV",ind[1],"(",round(va[1]*100,2),"%)"))+
             ylab(xlab(paste0("LV",ind[2],"(",round(va[2]*100,2),"%)")))
+        }
         p <- p + theme_classic(base_size =14)
     }
     if(type == "vip"){
@@ -368,8 +376,12 @@ plot.plsda <- function(x,type = "score",group = NULL,
         if(isTRUE(ellipse)&!is.null(group)){
             p <- p + stat_ellipse()
         }
+        if(ncol(dd)==1){
+            p <- p + xlab(paste0("LV",ind[1],"(",round(va[1]*100,2),"%)"))
+        }else{
         p <- p + xlab(paste0("LV",ind[1],"(",round(va[1]*100,2),"%)"))+
             ylab(xlab(paste0("LV",ind[2],"(",round(va[2]*100,2),"%)")))
+        }
         p <- p + theme_classic(base_size =14)
     }
     if(type == "vip"){