bugfix: label_scaffolds = TRUE ignored label_scaffolds_by and repel text

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Tools for extracting individual genomes from metagenomes
 Description: mmgenome: a toolbox for extracting individual genomes from
     metagenomes.
-Version: 2.0.7
+Version: 2.0.8
 Date: 2018-01-01
 Encoding: UTF-8
 Authors@R: c(person("Mads", "Albertsen", role = c("aut", "cre"), email = "MadsAlbertsen85@gmail.com"), person(c("Kasper", "Skytte"), "Andersen", role = c("aut"), email = "ksa@bio.aau.dk"), person(c("Rasmus", "Hansen"), "Kirkegaard", role = c("aut"), email = "rhk@bio.aau.dk"), person(c("Søren", "Michael"), "Karst", role = c("aut"), email = "smk@bio.aau.dk"))

R/mmplot.R

@@ -226,20 +226,24 @@ mmplot <- function(mm,
   }
 
   ##### label scaffolds #####
-  if(isTRUE(label_scaffolds)) {
-    p <- p + geom_text(label = mm[[1]], size = 4, color = "black")
-  } else if(is.vector(label_scaffolds) | is.data.frame(label_scaffolds)) {
+  if(!identical(FALSE, label_scaffolds)) {
+    #if label_scaffolds is a data frame, use the first column and expect them to be scaffolds names
     if(is.data.frame(label_scaffolds)) {
       label_scaffolds <- as.character(label_scaffolds[[1]])
     }
-    labels_data <- subset(mm, mm[[1]] %in% as.character(label_scaffolds))
+    #if label_scaffolds is TRUE label all
+    if(isTRUE(label_scaffolds))
+      label_scaffolds <- as.character(mm[[1]])
+    #label the provided scaffolds by label_scaffolds_by
+    labels_data <- subset(mm, mm[[1]] %in% label_scaffolds)
     p <- p + ggrepel::geom_text_repel(data = labels_data, 
                                       aes_(x = labels_data[[x]], 
                                            y = labels_data[[y]],
                                            label = labels_data[[label_scaffolds_by]]), 
                                       size = 4, 
                                       color = "black",
                                       inherit.aes = FALSE)
+
   }
 
   ##### Plot duplicates #####