diff --git a/R/make.clone.tree.grobs.R b/R/make.clone.tree.grobs.R
index 628777a..d81060b 100644
--- a/R/make.clone.tree.grobs.R
+++ b/R/make.clone.tree.grobs.R
@@ -1,4 +1,3 @@
-
 make.clone.tree.grobs <- function(
     ccf.df,
     tree,
diff --git a/R/set.up.plot.area.R b/R/set.up.plot.area.R
index 0e00707..b24eddd 100644
--- a/R/set.up.plot.area.R
+++ b/R/set.up.plot.area.R
@@ -15,15 +15,17 @@ calculate.main.plot.size <- function(
     node.radius
     ) {
 
-	ymax <- max(clone.out$v$len) + clone.out$v$y[1];
-	height <- (ymax) * scale1;
+    padding <- 2 * node.radius / scale1;
+    ymax <- clone.out$v$y[which.max(abs(clone.out$v$y))];
+	ymax <- ymax + (- sign(ymax) * padding);
+    height <- ymax * scale1;
 
     if (is.null(min.width)) {
         xmax <- wid;
         width <- wid * scale1 + 4 * node.radius;
         xlims <- c(
-            -(xmax / 2) - (2 * node.radius / scale1),
-            xmax / 2 + 2 * node.radius / scale1
+            -(xmax / 2) - padding,
+            xmax / 2 + padding
             );
     } else {
         xmin <- min(c(clone.out$v$x));
@@ -37,8 +39,8 @@ calculate.main.plot.size <- function(
             xmin <- xmin - 0.5 * diff / scale1
             xmax <- xmax + 0.5 * diff / scale1;
             xlims <- c(
-                xmin - (2 * node.radius / scale1),
-                xmax + 2 * node.radius / scale1
+                xmin - padding,
+                xmax + padding
                 );
 
             width <- (max(xlims) - min(xlims)) * scale1;
@@ -52,9 +54,7 @@ calculate.main.plot.size <- function(
 
 	clone.out$vp <- make.plot.viewport(
 	    clone.out,
-	    clip = if (clone.out$no.ccf) 'off' else 'on',
-	    just = c('centre', 'top'),
-	    y = 0.9
+	    clip = if (clone.out$no.ccf) 'off' else 'on'
 	    );
     }
 
@@ -247,6 +247,11 @@ add.yaxis <- function(
 
 	y.ticks.at <- ylabels / conversion.factor;
 
+	if (length(ylabels) == 0 || length(y.ticks.at) == 0) {
+        warning('No y-axis ticks to draw. Skipping axis rendering.');
+        return(ymax);
+        }
+
 	yaxis1 <- yaxisGrob(
 	    name = 'axis.content',
 	    at = y.ticks.at,
@@ -344,7 +349,8 @@ add.main <- function(
     size.units = 'npc'
     ) {
 
-	y.pos <- unit(1.08,'npc');
+	# y.pos <- unit(1.08,'npc');
+	y.pos <- unit(0.5,'npc');
 
 	if (!is.null(main.y)) {
 		pushViewport(clone.out$vp);
diff --git a/tests/testthat/data/branching.dendrogram.plots.Rda b/tests/testthat/data/branching.dendrogram.plots.Rda
index e15feca..38f25e0 100644
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diff --git a/tests/testthat/data/branching.fixed.plots.Rda b/tests/testthat/data/branching.fixed.plots.Rda
index aa8146c..8774cf5 100644
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diff --git a/tests/testthat/data/branching.radial.plots.Rda b/tests/testthat/data/branching.radial.plots.Rda
index 4112333..1addead 100644
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diff --git a/tests/testthat/data/linear.plots.Rda b/tests/testthat/data/linear.plots.Rda
index 33ca95e..a1ec3d0 100644
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