Create test.R

test/test.R

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+library(ggtree)
+library(tangler)
+library(ggnewscale)
+library(dplyr)
+library(ggplot2)
+
+tip_vec <- c('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M')
+
+t1 <- read.tree('../data/tree1.nwk')
+t2 <- read.tree('../data/tree2.nwk')
+
+#t1 <- rtree(n=13, tip.label = tip_vec)
+#t2 <- rtree(n=13, tip.label = tip_vec)
+
+#ape::write.tree(t1, file='~/Downloads/tree1.nwk')
+#ape::write.tree(t2, file='~/Downloads/tree2.nwk')
+
+meta <- read.csv(file = 'data/meta.csv')
+
+# Annotate Trees
+tree1 <- ggtree(t1)   %<+% meta +
+  geom_tiplab() +
+  geom_tippoint(aes(color=Genotype))
+
+
+tree2 <- ggtree(t2) %<+% meta + geom_tiplab()
+
+
+# Update the connecting line x-position so that it do not overlap with tip-labels.
+tangler::simple.tanglegram(tree1, tree2, Genotype, Green,  t2_pad = 0.3,
+                  tiplab = T, lab_pad = 0.1, x_hjust = 1, t2_tiplab_size = 3)
+
+# Rotate the internal nodes so that tips of both trees are aligned
+rotated_trees <- pre.rotate(t1, t2)
+
+t1 <- rotated_trees[[1]]
+t2 <- rotated_trees[[2]]
+
+# Annotate Trees, make sure to set ladderize=F
+tree1 <- ggtree(t1, ladderize=F)   %<+% meta +
+  geom_tiplab() +
+  geom_tippoint(aes(color=Genotype))
+
+# Annotate Tree 2
+tree2 <- ggtree(t2, ladderize=F) %<+% meta + geom_tiplab()
+
+
+# Tanglegram, no line color
+tangler::simple.tanglegram(tree1, tree2, Genotype, Green, t2_pad = 0.3,
+                           tiplab = T, lab_pad = 0.1, x_hjust = 1, t2_tiplab_size = 3)
+
+# Common tanglegram for both trait
+tangler::common.tanglegram(tree1, tree2, column = 'Genotype', sampletypecolors = c('green4', 'red'), t2_pad = 0.3,
+                           tiplab = T, lab_pad = 0.1, t2_tiplab_size = 3)
+
+
+# Patches issues
+# - Error in new_scale_color() : could not find function "new_scale_color"