add missing step to assign values to 'node.text'

R/add.text.R

@@ -497,8 +497,30 @@ add.text2 <- function(
     node.radius <- node.radius / scale;
     node.text <- node.text[node.text$node %in% tree$tip, ];
 
-    node.list <- data.frame(row.names = rownames(tree));
-    node.text.col <- node.text.fontface <- lapply
+    node.list <- vector("list", nrow(tree));
+    node.text.col <- vector("list", nrow(tree));
+    node.text.fontface <- vector("list", nrow(tree));
+
+    # Loop to assign text to nodes
+    for (i in seq_len(nrow(node.text))) {
+        text.row <- node.text[i, ];
+        pos <- which(tree$tip == text.row$node);
+        text.value <- text.row$name;
+
+        # Check if the text contains an underscore and parse if necessary
+        if (length(grep('_', text.value)) > 0) {
+            text.split <- strsplit(text.value, split = '_')[[1]];
+            node.text.value <- text.split[1];
+            amp <- text.split[2];
+            call <- paste0(node.text.value, '^\'A', amp, '\'');
+            text.value <- parse(text = call);
+            }
+
+        # Assign text value, color, and font face
+        node.list[[pos]] <- c(node.list[[pos]], text.value);
+        node.text.col[[pos]] <- c(node.text.col[[pos]], if (!is.na(text.row$col)) text.row$col else 'black');
+        node.text.fontface[[pos]] <- c(node.text.fontface[[pos]], if (!is.na(text.row$fontface)) text.row$fontface else 'plain');
+        }
 
     tree.max.adjusted <- apply(
         tree,
@@ -533,15 +555,15 @@ add.text2 <- function(
         );
     tree.max.adjusted$tipx <- (
         tree.max.adjusted$tipx -
-        -angle.modifier * node.radius * sin(tree.max.adjusted$angle)
+        angle.modifier * node.radius * sin(tree.max.adjusted$angle)
         );
     tree.max.adjusted$basey <- (
         tree.max.adjusted$basey +
         angle.modifier * node.radius * cos(tree.max.adjusted$angle)
         );
     tree.max.adjusted$tipy <- (
         tree.max.adjusted$tipy -
-        -angle.modifier * node.radius * cos(tree.max.adjusted$angle)
+        angle.modifier * node.radius * cos(tree.max.adjusted$angle)
         );
 
     # Push a viewport the same size as the final panel
@@ -552,7 +574,7 @@ add.text2 <- function(
         pushViewport(viewport(
             height = unit(panel.height, 'inches'),
             name = 'ref',
-            width = unit(panel.width,'inches'),
+            width = unit(panel.width, 'inches'),
             xscale = xlims,
             yscale = c(ymax, -2)
             ));
@@ -563,8 +585,8 @@ add.text2 <- function(
     tree.max.adjusted$y0 <- convertY(unit(tree.max.adjusted$basey, 'native'), 'inches', valueOnly = TRUE);
     tree.max.adjusted$y1 <- convertY(unit(tree.max.adjusted$tipy, 'native'), 'inches', valueOnly = TRUE);
 
-    tree.max.adjusted$y <- convertY(unit(tree.max$tipy, 'native'), 'inches', valueOnly = TRUE); # Actual node positions
-    tree.max.adjusted$x <- convertX(unit(tree.max$tipx, 'native'), 'inches', valueOnly = TRUE);
+    tree.max.adjusted$y <- convertY(unit(tree.max.adjusted$tipy, 'native'), 'inches', valueOnly = TRUE); # Actual node positions
+    tree.max.adjusted$x <- convertX(unit(tree.max.adjusted$tipx, 'native'), 'inches', valueOnly = TRUE);
 
     tree.max.adjusted$slope <- (tree.max.adjusted$y1 - tree.max.adjusted$y0) / (tree.max.adjusted$x1 - tree.max.adjusted$x0);
     tree.max.adjusted$intercept <- tree.max.adjusted$y1 - tree.max.adjusted$slope * tree.max.adjusted$x1;
@@ -597,7 +619,6 @@ add.text2 <- function(
             children = text.grob.gList,
             vp = make.plot.viewport(clone.out, clip = 'off')
             );
-
         return(text.tree);
         }
 
@@ -615,4 +636,4 @@ add.text2 <- function(
         );
 
     return(list(text.tree, tree.max.adjusted));
-	}
+    }