Answers.Body: <ol>
  <li><p>You can use <code>as.data.frame()</code> or <code>as_tibble()</code> to convert/coerce your matrix to a data frame or a tibble respectively (Technically a tibble is also a data frame). From there you should be fine with <code>ggplot()</code>.</p>
  </li>
  <li><p>I would not use a &quot;dynamite plot&quot; (this is a box plot with error bars like the one in your question), that type of plots conceal the data! <a href="https://simplystatistics.org/2019/02/21/dynamite-plots-must-die/" rel="nofollow noreferrer">This post</a> explains why and remedies.</p>
  </li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-16T19:41:27.543Z
Answers.LastActivityDate: 2021-06-17T10:38:50.197Z
Answers.LastEditDate: 2021-06-17T10:38:50.197Z
Answers.UserDisplayName: haci
Body: <p>I'm trying to generate boxplot from Beta diversity boxplot between two conditions from a phyloseq object.</p>
  <p>I have a Morisita-horn distance generated by vegdist fonction :</p>
  <pre><code>vegdist&lt;-vegdist(t(otu_table(physeq_genus_3a)), method=&quot;horn&quot;)#matrice distance Morisita-horn
  vegdist&lt;-as.matrix(vegdist)
  </code></pre>
  <p>Now I have a matrix and I would like to somewhat create a mean distance boxplot of the Morisita-horn index winthin two condition like the graph below.</p>
  <p>I wanted to do a simple boxplot with ggplot but beacause it is a matrix and not a dataframe, I can't do it.</p>
  <p>Any help or suggestions would be more than welcome.</p>
  <p><a href="https://i.sstatic.net/8bUl6.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/8bUl6.jpg" alt="enter image description here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-06-16T12:07:01.447Z
Comments.Text: Could you please show a bit more of your data, or another test dataset? It would be greate if you could provide enough that we could use it to create a bar plot with error bars.
Comments.UserDisplayName: gringer
Tags: <r><microbiology><graphs><phyloseq>
Title: How to create Beta Diversity distance boxplot
ThreadText: # How to create Beta Diversity distance boxplot
  
  (Asked by: username_0 on 2021-06-16)
  
  I'm trying to generate boxplot from Beta diversity boxplot between two conditions from a phyloseq object.
  
  I have a Morisita-horn distance generated by vegdist fonction :
  
  ```
  vegdist<-vegdist(t(otu_table(physeq_genus_3a)), method="horn")#matrice distance Morisita-horn
  vegdist<-as.matrix(vegdist)
  
  ```
  
  Now I have a matrix and I would like to somewhat create a mean distance boxplot of the Morisita-horn index winthin two condition like the graph below.
  
  I wanted to do a simple boxplot with ggplot but beacause it is a matrix and not a dataframe, I can't do it.
  
  Any help or suggestions would be more than welcome.
  
  [![enter image description here](https://i.sstatic.net/8bUl6.jpg)](https://i.sstatic.net/8bUl6.jpg)
  
  **Tags:** r, microbiology, graphs, phyloseq
  
  > **Comments:**
  > **username_1**: Could you please show a bit more of your data, or another test dataset? It would be greate if you could provide enough that we could use it to create a bar plot with error bars.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-06-16. Score: 1
  
  1. You can use `as.data.frame()` or `as_tibble()` to convert/coerce your matrix to a data frame or a tibble respectively (Technically a tibble is also a data frame). From there you should be fine with `ggplot()`.
  2. I would not use a "dynamite plot" (this is a box plot with error bars like the one in your question), that type of plots conceal the data! [This post](https://simplystatistics.org/2019/02/21/dynamite-plots-must-die/) explains why and remedies.
  
  
  ---
  
  