Merge pull request #85 from jasenfinch/devel

v0.14.8

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
-Version: 0.14.7
+Version: 0.14.8
 Authors@R: person("Jasen", "Finch", email = "[email protected]", role = c("aut", "cre"))
 Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
 URL: https://jasenfinch.github.io/metabolyseR

NEWS.md

@@ -1,3 +1,9 @@
+# metabolyseR 0.14.8
+
+* An error is now thrown during random forest classification when less than two classes are specified.
+
+* [`plotSupervisedRF()`](https://jasenfinch.github.io/metabolyseR/reference/plotSupervisedRF.html) now skips plotting if errors are encountered during random forest training.
+
 # metabolyseR 0.14.7
 
 * Single replicate classes now automatically removed by [`plotLDA()`](https://jasenfinch.github.io/metabolyseR/reference/plotLDA.html).

R/plotSupervisedRF.R

@@ -59,35 +59,39 @@ setMethod('plotSupervisedRF',
                    legendPosition = 'bottom', 
                    labelSize = 2){
 
-            rf <- randomForest(x,
+            rf <- try(randomForest(x,
                                cls = cls,
                                rf = rf,
                                reps = 1,
-                               seed = seed)
+                               seed = seed))
 
-            pl <- plotMDS(rf,
-                          cls = cls,
-                          label = label,
-                          ellipses = ellipses,
-                          title = '',
-                          legendPosition = legendPosition,
-                          labelSize = labelSize) +
-              labs(
-                caption = str_c('Margin: ',
-                                rf@results$measures$.estimate[4] %>% 
-                                  round(3)))
-
-            if (isTRUE(ROC) & rf@type == 'classification') {
-              pl <- pl + 
-                plotROC(rf,legendPosition = legendPosition) + 
-                plot_annotation(
-                  title = title,
-                  theme = theme(plot.title = element_text(face = 'bold')))
+            if (class(rf) != 'try-error') {
+              pl <- plotMDS(rf,
+                            cls = cls,
+                            label = label,
+                            ellipses = ellipses,
+                            title = '',
+                            legendPosition = legendPosition,
+                            labelSize = labelSize) +
+                labs(
+                  caption = str_c('Margin: ',
+                                  rf@results$measures$.estimate[4] %>% 
+                                    round(3)))
+
+              if (isTRUE(ROC) & rf@type == 'classification') {
+                pl <- pl + 
+                  plotROC(rf,legendPosition = legendPosition) + 
+                  plot_annotation(
+                    title = title,
+                    theme = theme(plot.title = element_text(face = 'bold')))
+              } else {
+                pl <- pl + labs(title = title)
+              }
+
+              return(pl) 
             } else {
-              pl <- pl + labs(title = title)
+              warning('Errors encounted in random forest training, skipping plotting of supervised random forest.',call. = FALSE)
             }
-
-            return(pl)
           }
 )
 

R/randomForest.R

@@ -460,18 +460,25 @@ classification <- function(x,
                       select(all_of(cls)) %>%
                       deframe())
 
+    cls_list <- clsRem %>%
+      select(all_of(cls)) %>%
+      deframe() %>%
+      str_c('"',.,'"') %>% 
+      str_c(.,collapse = ', ')
+
     warning(str_c('Classes with < 5 replicates removed: ',
-                  str_c(str_c('"',clsRem %>%
-                                select(all_of(cls)) %>%
-                                deframe(),
-                              '"'),collapse = ', ')),
+                  cls_list),
             call. = FALSE)
 
     i <- x %>%
       sinfo() %>%
       select(cls)
   }
 
+  if (length(unique(deframe(i))) < 2) {
+   stop('Need at least two classes to do classification.',call. = FALSE) 
+  }
+
   if (length(comparisons) > 0) {
     comp <- comparisons
   } else {