@@ -10,7 +10,7 @@ Maintainer: Dario Strbenac <dario.strbenac@sydney.edu.au>

 VignetteBuilder: knitr

 Encoding: UTF-8

 biocViews: Classification, Survival

-Depends: R (>= 4.1.0), generics, methods, S4Vectors (>= 0.18.0), MultiAssayExperiment (>= 1.6.0), BiocParallel, survival

+Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival

 Imports: grid, genefilter, utils, dplyr, tidyr, rlang, randomForest

 Suggests: limma, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0), gridExtra (>= 2.0.0), cowplot,

         BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable,

@@ -171,6 +171,12 @@ setMethod("plotFeatureClasses", "DataFrame", function(measurements, classes, use

     groupBy <- list(legends = factor(groupBy, levels = levelsOrder),

                     facets = factor(paste(groupingName, "is", groupBy), levels = paste(groupingName, "is", levelsOrder)))

   }

+  if(is.character(classes) || is.integer(classes))

+    classes <- measurements[, classes] # Otherwise an independent factor.

+  if(is.character(classes)) classes <- factor(classes)

+

+  if(length(colours) != length(levels(classes)))

+    colours <- scales::hue_pal()(length(levels(classes)))

   if(!requireNamespace("ggplot2", quietly = TRUE))

     stop("The package 'ggplot2' could not be found. Please install it.")

@@ -57,6 +57,7 @@ setMethod("prepareData", "DataFrame",

   # Won't ever be true if input data was MultiAssayExperiment because wideFormat already produces valid names.  

   if(all.equal(colnames(measurements), make.names(colnames(measurements))) != TRUE)

   {

+    warning("Unsafe feature names in input data. Converted into safe names.")

     mcols(measurements)$feature <- colnames(measurements) # Save the originals.

     colnames(measurements) <- make.names(colnames(measurements)) # Ensure column names are safe names.

   }