fix broken vigettes

groups slot for pca scores is no longer usedis deprecated

Author: grlloyd

R/PCA_plotfcns.R

@@ -69,7 +69,7 @@ pca_scores_plot<-setClass(
         params.factor_name='entity',
         params.ellipse='enum',
         params.label_filter='entity',
-        params.groups='factor'
+        params.groups='ANY' # will be deprecated
     ),
 
     prototype = list(name='PCA scores plot',

vignettes/method_example.Rmd

@@ -57,7 +57,7 @@ MVA = model.train(MVA,predicted(PMP))
 MVA = model.predict(MVA,predicted(PMP))
 
 # charts
-C = pca_scores_plot(factor_name = 'Class',groups=D$sample_meta$class)
+C = pca_scores_plot(factor_name = 'class',groups=D$sample_meta$class)
 chart.plot(C,MVA[2])
 ```
 
@@ -149,7 +149,7 @@ MVA2 = model.train(MVA2,predicted(MS2))
 MVA2 = model.predict(MVA2,predicted(MS2))
 
 # charts
-C = pca_scores_plot(factor_name = 'Class',groups=D$sample_meta$class)
+C = pca_scores_plot(factor_name = 'class',groups=D$sample_meta$class)
 chart.plot(C,MVA2[2])
 ```
 

vignettes/model_example.Rmd

@@ -105,7 +105,9 @@ chart.plot(C,M[2])
 If we makes changes to our chart object, we must call `chart.plot` again.
 
 ```{r}
-C$groups = D$data$Petal.Width
+# add petal width to emta data of pca scores
+M[2]$scores$sample_meta$Petal.Width=D$data$Petal.Width
+# update plot
 C$factor_name='Petal.Width'
 chart.plot(C,M[2])
 ```