Answers.Body: <p>I suspect the solution is to realign the two plots within "ggarrange", available <a href="https://www.rdocumentation.org/packages/ggpubr/versions/0.2/topics/ggarrange" rel="nofollow noreferrer">here</a></p>
  
  <p>The problem is stacking ggtree with geom_tiplab. The ggarrange library is described on STHDA <a href="http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/81-ggplot2-easy-way-to-mix-multiple-graphs-on-the-same-page/" rel="nofollow noreferrer">here</a>  </p>
  
  <p>I have not used this library however, but it should be easy because you are working singly within R. I tend to use ggplot2 within Python via rpy2, which is much more difficult and restricted. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-16T17:21:32.333Z
Answers.LastActivityDate: 2019-06-18T15:00:47.333Z
Answers.LastEditDate: 2019-06-18T15:00:47.333Z
Answers.UserDisplayName: M__
Answers.Body: <p>You were very close, you just need to supply the <code>offset</code> argument to <code>msaplot()</code>.</p>
  
  <p>So using your code block above with one extra argument in <code>msaplot()</code></p>
  
  <pre><code>library(tidyverse)
  library(ggtree) 
  library(seqinr)
  tree = read.tree("din.newick") 
  msaplot(p=ggtree(tree), fasta = "din.fasta")
  msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta", offset = 5)
  </code></pre>
  
  <p>yields</p>
  
  <p><a href="https://i.sstatic.net/3thEk.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/3thEk.png" alt="msaplot with offset"></a></p>
  
  <p>Thank you for supplying a minimal and reproducible example!</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-18T04:45:34.043Z
Answers.Text: Thank you @Kohl Kinning.
Answers.UserDisplayName: Kumar
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-17T16:14:55.147Z
Answers.LastActivityDate: 2019-06-17T16:14:55.147Z
Answers.UserDisplayName: Kohl Kinning
Body: <p>I would like to visualize tree with multiple sequence alignment. 
  My <code>din.newick</code> file is shown below,</p>
  
  <pre><code>(org1:0.49999997,org2:0.47298786,org3:28.37858179);
  </code></pre>
  
  <p>My <code>din.fasta</code> alignment file shown below,</p>
  
  <pre><code>&gt;org1
  ATGCTA
  &gt;org2
  TAGCAT
  &gt;org3
  AGTAGT
  </code></pre>
  
  <p>I have tried the following code,</p>
  
  <pre><code>library(tidyverse)
  library(ggtree) 
  library(seqinr)
  tree = read.tree("din.newick") 
  msaplot(p=ggtree(tree), fasta = "din.fasta")
  msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta")
  </code></pre>
  
  <p>The above mentioned code is generating tree with the alignment matrix, but the tree root tip labels are not visible. It is either overlapped with matrix or it is not at all visible. <a href="https://i.sstatic.net/y9LbQ.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/y9LbQ.jpg" alt="msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = &quot;din.fasta&quot;)"></a> Kindly help me to fix this issue. </p>
  
Tags: <r><bioconductor><fasta><phylogenetics><phylogeny>
Title: Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
ThreadText: # Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
  
  (Asked by: username_0 on 2019-06-16)
  
  I would like to visualize tree with multiple sequence alignment.
  My `din.newick` file is shown below,
  
  ```
  (org1:0.49999997,org2:0.47298786,org3:28.37858179);
  
  ```
  
  My `din.fasta` alignment file shown below,
  
  ```
  >org1
  ATGCTA
  >org2
  TAGCAT
  >org3
  AGTAGT
  
  ```
  
  I have tried the following code,
  
  ```
  library(tidyverse)
  library(ggtree) 
  library(seqinr)
  tree = read.tree("din.newick") 
  msaplot(p=ggtree(tree), fasta = "din.fasta")
  msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta")
  
  ```
  
  The above mentioned code is generating tree with the alignment matrix, but the tree root tip labels are not visible. It is either overlapped with matrix or it is not at all visible. [![msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta")](https://i.sstatic.net/y9LbQ.jpg)](https://i.sstatic.net/y9LbQ.jpg) Kindly help me to fix this issue.
  
  **Tags:** r, bioconductor, fasta, phylogenetics, phylogeny
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2019-06-17. Score: 4 | Accepted answer
  
  You were very close, you just need to supply the `offset` argument to `msaplot()`.
  
  So using your code block above with one extra argument in `msaplot()`
  
  ```
  library(tidyverse)
  library(ggtree) 
  library(seqinr)
  tree = read.tree("din.newick") 
  msaplot(p=ggtree(tree), fasta = "din.fasta")
  msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta", offset = 5)
  
  ```
  
  yields
  
  [![msaplot with offset](https://i.sstatic.net/3thEk.png)](https://i.sstatic.net/3thEk.png)
  
  Thank you for supplying a minimal and reproducible example!
  
  > **Comments:**
  > **username_0**: Thank you @username_2.  
  
  ---
  
  ### Answer by username_1 on 2019-06-16. Score: 0
  
  I suspect the solution is to realign the two plots within "ggarrange", available [here](https://www.rdocumentation.org/packages/ggpubr/versions/0.2/topics/ggarrange)
  
  The problem is stacking ggtree with geom\_tiplab. The ggarrange library is described on STHDA [here](http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/81-ggplot2-easy-way-to-mix-multiple-graphs-on-the-same-page/)
  
  I have not used this library however, but it should be easy because you are working singly within R. I tend to use ggplot2 within Python via rpy2, which is much more difficult and restricted.
  
  
  ---
  
  