Read node sizes and transparency for ML tree from design script

Also removes an unused variable

Author: ahmig

config/design_plots.R

@@ -43,22 +43,15 @@ gene_colors = c(
 
 # M-L tree colors and labels
 tree_colors = c(
-  tip_label = "#D944AA",
-  boot_alrt_pass = "#64acee"
+  tip_label = "#D944AA99",
+  boot_alrt_pass = "#64ACEEB2"
 )
 
-
 node.size <- c(
   tip_label = 2,
   boot_alrt_pass = 0.8
 )
 
-node.alpha <- c(
-  tip_label = 0.6,
-  boot_alrt_pass = 0.7
-)
-
-
 # Nucleotide variants classification colors and labels
 NV_colors <- c(
   Frameshift = "#568D63",

workflow/scripts/report/phylo_plots.R

@@ -245,7 +245,10 @@ p <- ggtree(tree_ml, layout = "circular") %<+% ml.tree.annot +
     values = setNames(tree_colors[names(legend.names)], legend.names),
     na.translate = FALSE
   ) +
-  scale_size_discrete(range = c(2, 1), na.translate = FALSE)
+  scale_size_manual(
+    values = setNames(node.size[names(legend.names)], legend.names),
+    na.translate = FALSE
+  )
 
 ggsave(
   filename = snakemake@output[["tree_ml"]],