housekeeping

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: mixOmics
 Type: Package
 Title: Omics Data Integration Project
-Version: 6.17.17
+Version: 6.17.18
 Depends: R (>= 3.5.0), 
          MASS, 
          lattice, 

R/helpers-plot.R

@@ -149,10 +149,12 @@
         if (nlevels(group) == 1)
         {
             col.per.group <- ifelse(is.null(col), color.mixo(1), .are.colors(col))
-        }
-        else
-        { ## group is of length >= 2
+        } else if (nlevels(group) < 10)
+        { 
             col.per.group <- color.mixo(seq_len(nlevels(group)))
+        } else if (nlevels(group) >= 10)
+        { 
+            col.per.group <- color.jet(nlevels(group))
         }
 
         names(col.per.group) <- levels(group)

R/plotIndiv.R

@@ -70,8 +70,7 @@
 #' for ellipse plots. Coded as default for the supervised methods \code{PLS-DA,
 #' SPLS-DA,sGCCDA}, but needs to be input for the unsupervised methods
 #' \code{PCA, sPCA, IPCA, sIPCA, PLS, sPLS, rCC, rGCCA, sGCCA}
-#' @param col.per.group character (or symbol) color to be used when 'group' is
-#' defined. Vector of the same length as the number of groups.
+#' @template arg/col.per.group
 #' @param style argument to be set to either \code{'graphics'},
 #' \code{'lattice'}, \code{'ggplot2'} or \code{'3d'} for a style of plotting.
 #' Default set to 'ggplot2'. See details. \code{3d} is not available for MINT

R/selectVar.R

@@ -133,15 +133,13 @@ selectVar.sgcca <- selectVar.mixo_pls
 selectVar.rgcca <- selectVar.mixo_pls
 
 ## -------------------------------- helper -------------------------------- ##
-get.name.and.value=function(x,comp)
+get.name.and.value <- function(x,comp)
 {
-    if(length(x[,comp,drop=FALSE]) > 1)
-    {
-        name.var = names(sort(abs(x[,comp]), decreasing = TRUE)[1:sum(x[,comp]!=0)])
-    } else {
-        name.var = rownames(x) # when only one number, sort loses the name of the variable
-    }
-    value.var=x[name.var,comp]
-    return(list(name = name.var, value = data.frame(value.var)))
+    value <- data.frame(value.var = x[,comp])
+    value <- value[abs(value$value.var) > .Machine$double.eps,,drop=FALSE]
+    value <- value[order(-abs(value$value.var)),,drop=FALSE]
+
+    name.var <- rownames(value)
+    return(list(name = name.var, value = value))
 }