Comments on: Merging a phylogenetic tree with a heatmap in R

By: Jeff

Jeff — Thu, 11 Mar 2021 05:34:01 +0000

In reply to Jaber Abbaszadeh. Great, thanks for sharing! This tutorial is pretty outdated now :)

By: Jaber Abbaszadeh

Jaber Abbaszadeh — Thu, 11 Mar 2021 03:49:36 +0000

Hi Jeff.
I used your method to combine a phylogenetic tree and heatmap and it worked! However, there are some inconsistencies. For example, the order of tree tips was changed in the final tree + heatmap compared with the tree itself.
I found an easier way to draw the tree with a heatmap.
The ggtree and ggtreeExtra packages offer gheatmap() function and you can draw your tree+heatmap with only one line. ggtreeExtra is helpful with circular trees + heatmap + barplots ….

By: Jeff

Jeff — Wed, 13 Jan 2016 22:08:04 +0000

In reply to ygc. That looks great, thanks for the tip!

By: ygc

ygc — Wed, 13 Jan 2016 07:09:33 +0000

use ggtree, , will make your life more easier.

By: Jeff

Jeff — Sun, 08 Nov 2015 14:02:26 +0000

In reply to heavennew. Use the root() command, and either specify a node or use the interactive option to select a node. Typically you want the tree to be rooted at the node from which the outgroup diverges from the rest of the sequences.

By: heavennew

heavennew — Sat, 07 Nov 2015 18:42:08 +0000

In reply to Jeff. Hi, Jeff, I do not know how do you made the rooted phylogenetic tree with R and how do you choose the node of root.(For the root I selected the node between the two Archaea and Planctomyces).

By: Jeff

Jeff — Thu, 04 Jun 2015 13:36:06 +0000

Yes, there seems to be something strange in your input file – R won’t even read that tree in. It did read in, with a warning, to Archaeopteryx. Arbitrarily rerooting the tree in Archaeopteryx produced a tree that read fine into R (below). I suggest using the following and re-rooting within R. Good luck!

((((((Mt3.5v5,Mt4.0v1),Car),(((Pvu186,Pvu218),(Gma109,Gma189)),Cca))),(((Ppe139,Mdo196),Fve226),Csa122)),((((((((((Cre169,Vca199),Csu227),((Mpu228,Mpu229),Olu231)),Ppa152),Smo91),(((Sbi79,Zma181),(Sit164,Pvi202)),(Osa193,Bdi192))),Aco195),((Stu206,Sly225),Mgu140)),Vvi145),((((((((Ath167,Aly107),Cru183),(Bra197,Tha173)),Cpa113),(Gra221,Tca233)),(Csi154,(Ccl165,Ccl182))),((Mes147,Rco119),(Lus200,(Ptr156,Ptr210)))),Egr201)));

By: Anand

Anand — Thu, 04 Jun 2015 04:38:11 +0000

Hi John,
I am trying your step rep_tree_r mytree_brlen plot(tree,edge.width=3,lend=2)
Error in plot.phylo(tree, edge.width = 3, lend = 2) :
there are single (non-splitting) nodes in your tree; you may need to use collapse.singles()

So followed instructions suggested at http://blog.phytools.org/2013/06/robust-newick-tree-reader.html?showComment=1433380847966#c1946368120991641492
> tree=collapse.singles(tree)
> plot(tree,edge.width=3,lend=2)
But this tree looks completely mangled….

So I suspect the problem is with my .tre input file (copied and posted below)
Could you please help me identify the problem so that I can move ahead with my analysis?
The goal of this is to convert my species cladogam to a dendrogram that I can use as the column dendrogram for my heatmap

(((((((((((((Mt3.5v5, Mt4.0v1), Car), (((Pvu186, Pvu218), (Gma109, Gma189)), Cca))), (((Ppe139, Mdo196), Fve226), Csa122)), ((((((((Ath167, Aly107), Cru183), (Bra197, Tha173)), Cpa113), (Gra221, Tca233)), (Csi154, (Ccl165, Ccl182))), ((Mes147, Rco119),(Lus200, (Ptr156, Ptr210)))), Egr201)), Vvi145), ((Stu206, Sly225), Mgu140)), Aco195), (((Sbi79, Zma181),(Sit164, Pvi202)), (Osa193, Bdi192))), Smo91), Ppa152), (((Cre169, Vca199), Csu227), ((Mpu228, Mpu229), Olu231)));

Thank you!