Data frame error when visualizing tree with MSA on different Newick tree file

[Benjy Jek Yang Tan]

Hi, 

I was wondering if you could help me with this error.

I was trying to visualize a MSA together with my tree using 2 different Newick tree files. On the first one, I was able to make the figure. 

However, when I used it on the second Newick file, with the same FASTA file, I received an error as below.

Error in data.frame(name = names(seqs)[i], xmin = xmin, xmax = xmax, ymin = ymin[i],  : arguments imply differing number of rows: 1, 8985, 0

I tried to look into the error but I don't really understand what caused this error as I was using the same FASTA file. 

Could it be because of the strange results of Newick2.nwk?

I attached the Newick files and FASTA file I used as below.

Hope to hear back soon. Thank you very much.

[Yu, Guangchuang]

if you use latest version of ggtree, it will throw the following error:

Error in msaplot(ggtree(y), fa) :
  taxa name in input sequences are not match with the ones on the tree, please check your input files...

Based on this msg, you should know what’s going on here.

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1. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
 
2. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194
 
Homepage: https://guangchuangyu.github.io/software/ggtree
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Guangchuang Yu PhD

Professor
School of Basic Medical Sciences

Southern Medical University

Guangzhou, China

www: https://guangchuangyu.github.io

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[Benjy Jek Yang Tan]

Thank you Prof. Yu for your prompt reply. 

I see now. That makes things clearer. I will have a look at it. 

However, just to note, I am using the latest version of ggtree (1.14.4) and also the latest version of R. But I did not see the message as mentioned by you. Perhaps there is a bug somewhere? 

[Benjy Jek Yang Tan]

Thank you very much for your reply. 

I was able to solve the issue. It was indeed a mistake of inconsistent taxa name. 

Thanks again!