How to connect the tips of several phylogenetic trees with ggtree?

Question

[Luca Arbore]

I am trying to build a tanglegram of 4 gene trees from a segmented virus genome. I have followed the package manual as per subcap. 2.6: https://yulab-smu.top/treedata-book/chapter2.html but I am getting connecting lines not only between tips, but nodes as well.

I suspect it has to do with filtering of label, since I tried in fortify() to use only is.Tip, and I get the correct labels and lines, but no trees.

Any help would be greatly appreaciated.

s1 <- read.tree(here("data/jingmen_s1_pool1.fasta.treefile"))
s2 <- read.tree(here("data/jingmen_s2_pool1.fasta.treefile"))
s3 <- read.tree(here("data/jingmen_s3_pool1.fasta.treefile"))
s4 <- read.tree(here("data/jingmen_s4_pool1.fasta.treefile"))

tree1 <- fortify(s1)
tree2 <- fortify(s2)
tree3 <- fortify(s3)
tree4 <- fortify(s4)
tree2$x <- tree2$x + max(tree1$x) +.1
tree3$x <- tree3$x + max(tree2$x) +.1
tree4$x <- tree4$x + max(tree3$x) +.1
jingmen_s <- bind_rows(tree1, tree2, tree3, tree4) %>%
filter(!is.na(label))

p <- ggtree(tree1) +
geom_tree(data = tree2) +
geom_tree(data = tree3) +
geom_tree(data = tree4) +
geom_tiplab(data = tree1) +
geom_tiplab(data = tree2, hjust = 0) +
geom_tiplab(data = tree3, hjust = 0) +
geom_tiplab(data = tree4, hjust = 0) +
geom_line( 
aes(x, y, group = label),
data = jingmen_s,
alpha = 0.5 
)

[Dunois]

Can you please share the data that's stored in jingmen_s? My guess is that the filter() function hasn't worked here as intended.

[Luca Arbore]

I could not find an attach button so here they are. thank you.

jingmen_s1_pool1.fasta.treefile:  
(141_03-Ixodes:0.0058790622,(141_31-Amblyomma:0.0048478844,141_22-Amblyomma:0.0067408617)44:0.0006327728,((141_11-Amblyomma:0.0022375969,141_24-Amblyomma:0.0025573326)99:0.0037176841,((143_56-Amblyomma:0.0067582270,143_58-Amblyomma:0.0074819674)50:0.0003078880,((((141_20-Amblyomma:0.0064174548,141_30-Amblyomma:0.0064542266)100:0.0120856690,(143_76-Amblyomma:0.0048197795,143_97-Ixodes:0.0094804061)100:0.0065997540)95:0.0036604520,143_51-Ixodes:0.0221693904)78:0.0014915317,(141_45-Amblyomma:0.0169051121,(141_32-Amblyomma:0.0297678872,141_38-Amblyomma:0.0143533575)100:0.0190918589)62:0.0018350031)100:0.0224227073)54:0.0003599291)41:0.0000010000);

jingmen_s2_pool1.fasta.treefile:
(141_03-Ixodes:0.0083569432,(((141_11-Amblyomma:0.0044526766,((((((141_20-Amblyomma:0.0138174359,141_30-Amblyomma:0.0111721230)100:0.0072570030,(143_51-Ixodes:0.0130237457,(143_76-Amblyomma:0.0044946052,143_97-Ixodes:0.0040635289)98:0.0038309260)97:0.0043972545)98:0.0057358005,141_45-Amblyomma:0.0152997386)100:0.0346705100,141_32-Amblyomma:0.0059771409)87:0.0035729200,(141_31-Amblyomma:0.0060252413,141_38-Amblyomma:0.0078595820)89:0.0027194542)76:0.0009500542,141_22-Amblyomma:0.0059485391)73:0.0008345897)69:0.0013085051,141_24-Amblyomma:0.0055641651)60:0.0009751494,143_58-Amblyomma:0.0059794758)43:0.0008332118,143_56-Amblyomma:0.0050462446);

jingmen_s3_pool1.fasta.treefile:
(141_03-Ixodes:0.0061443854,(((141_11-Amblyomma:0.0283177144,141_24-Amblyomma:0.0003156453)99:0.0023094277,(((((((141_20-Amblyomma:0.0086982000,141_30-Amblyomma:0.0078430199)100:0.0070082674,(143_76-Amblyomma:0.0074656681,143_97-Ixodes:0.0327668676)72:0.0004674880)99:0.0044802711,143_51-Ixodes:0.0036352988)99:0.0042266426,141_32-Amblyomma:0.0325733571)88:0.0024957315,(141_45-Amblyomma:0.0122030800,143_58-Amblyomma:0.0125810341)76:0.0011932194)96:0.0026569622,141_38-Amblyomma:0.0077671160)93:0.0016380152,141_31-Amblyomma:0.0084611791)98:0.0038790835)74:0.0006385019,141_22-Amblyomma:0.0053788355)99:0.0032965711,143_56-Amblyomma:0.0037627578);

jingmen_s4_pool1.fasta.treefile:
(141_03-Ixodes:0.0028255604,(((((141_11-Amblyomma:0.0061816798,141_38-Amblyomma:0.0047904531)99:0.0049092032,(((((141_20-Amblyomma:0.0140752466,143_97-Ixodes:0.0125111638)86:0.0025622480,143_76-Amblyomma:0.0213522193)96:0.0085784636,143_51-Ixodes:0.0344050862)97:0.0081899459,(141_30-Amblyomma:0.0167873007,141_45-Amblyomma:0.0099544344)100:0.0165199255)100:0.0100142165,141_24-Amblyomma:0.0076510655)79:0.0012183343)96:0.0032101202,143_56-Amblyomma:0.0076468089)99:0.0039165629,(141_31-Amblyomma:0.0056549381,141_32-Amblyomma:0.0021457820)72:0.0003747946)98:0.0023547931,143_58-Amblyomma:0.0037407301)60:0.0003084861,141_22-Amblyomma:0.0018630146);

Answer 1

[Luca Arbore]

Solved! Tips have to be included in the filter

jingmen_s <- bind_rows(tree1, tree2, tree3, tree4) %>%
filter(!is.na(label) & isTip == TRUE)