Answers.Body: <p>I assume you are referring to <code>VlnPlot()</code> of Seurat. The reason that you are getting such a plot is because your distribution is highly skewed, most of your points are zeros, not surprising for scRNA-seq. And the plot is actually showing your distributions, it is just the points at zero stacking on top of each other.</p>
  
  <p>You can double check this by plotting a histogram for each of the clusters.</p>
  
  <p>An example violin plot:</p>
  
  <p><a href="https://i.sstatic.net/BMK1r.png" rel="noreferrer"><img src="https://i.sstatic.net/BMK1r.png" alt="enter image description here"></a></p>
  
  <p>Cluster 0, which is mostly zeros, kind of looks like yours.</p>
  
  <p><a href="https://i.sstatic.net/0oMTG.png" rel="noreferrer"><img src="https://i.sstatic.net/0oMTG.png" alt="enter image description here"></a></p>
  
  <p>Cluster 6, which I believe is what you would expect to see, contains a lot of cells that express the gene and much less skewed, hence the shape denoting the density.</p>
  
  <p><a href="https://i.sstatic.net/kBC32.png" rel="noreferrer"><img src="https://i.sstatic.net/kBC32.png" alt="enter image description here"></a></p>
  
  <p>So what you are seeing is normal, your gene is not expressed/not detected is all.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-19T21:20:41.470Z
Answers.LastActivityDate: 2018-10-20T08:03:06.593Z
Answers.LastEditDate: 2018-10-20T08:03:06.593Z
Answers.UserDisplayName: haci
Answers.Body: <p>Try using ridgeplots instead of violin plots.  Ridge plots will show you that bump at zero</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-07T17:08:39.090Z
Answers.LastActivityDate: 2021-01-07T17:08:39.090Z
Answers.UserDisplayName: swbarnes2
Body: <p>I was confused about the VlnPlot that it shows like the screenshot. It only shows the dot but no distribution of the data, is that normal?<a href="https://i.sstatic.net/CYjGQ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/CYjGQ.png" alt="enter image description here"></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-31T20:03:34.890Z
Comments.Text: Hello Hua, welcome to bioinformatics.SE. If you search google images for "Vln Plot", you find how it should look like, [for instance](https://github.com/satijalab/seurat/issues/82). We are happy to help with questions, but we kindly ask people to devote some effort in resolving problem by their own and showing the research effort in the question. Also note that we don't see your data, it's very hard to guess what is wrong with your plots without it. My guess is that you have vast vast majority of data points == 0.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-07T11:01:56.330Z
Comments.Text: But is it possible to show the distribution for lowly expressed genes? How can I manually set the parameters in vlnplot() function to show the contours?
Comments.UserDisplayName: Shanlin Tong
Tags: <scrnaseq>
Title: VlnPlot problem
ThreadText: # VlnPlot problem
  
  (Asked by: username_0 on 2018-08-31)
  
  I was confused about the VlnPlot that it shows like the screenshot. It only shows the dot but no distribution of the data, is that normal?[![enter image description here](https://i.sstatic.net/CYjGQ.png)](https://i.sstatic.net/CYjGQ.png)
  
  **Tags:** scrnaseq
  
  > **Comments:**
  > **username_1**: Hello Hua, welcome to bioinformatics.SE. If you search google images for "Vln Plot", you find how it should look like, [for instance](https://github.com/satijalab/seurat/issues/82). We are happy to help with questions, but we kindly ask people to devote some effort in resolving problem by their own and showing the research effort in the question. Also note that we don't see your data, it's very hard to guess what is wrong with your plots without it. My guess is that you have vast vast majority of data points == 0.  
  > **username_2**: But is it possible to show the distribution for lowly expressed genes? How can I manually set the parameters in vlnplot() function to show the contours?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2018-10-19. Score: 6
  
  I assume you are referring to `VlnPlot()` of Seurat. The reason that you are getting such a plot is because your distribution is highly skewed, most of your points are zeros, not surprising for scRNA-seq. And the plot is actually showing your distributions, it is just the points at zero stacking on top of each other.
  
  You can double check this by plotting a histogram for each of the clusters.
  
  An example violin plot:
  
  [![enter image description here](https://i.sstatic.net/BMK1r.png)](https://i.sstatic.net/BMK1r.png)
  
  Cluster 0, which is mostly zeros, kind of looks like yours.
  
  [![enter image description here](https://i.sstatic.net/0oMTG.png)](https://i.sstatic.net/0oMTG.png)
  
  Cluster 6, which I believe is what you would expect to see, contains a lot of cells that express the gene and much less skewed, hence the shape denoting the density.
  
  [![enter image description here](https://i.sstatic.net/kBC32.png)](https://i.sstatic.net/kBC32.png)
  
  So what you are seeing is normal, your gene is not expressed/not detected is all.
  
  
  ---
  
  ### Answer by username_4 on 2021-01-07. Score: 0
  
  Try using ridgeplots instead of violin plots. Ridge plots will show you that bump at zero
  
  
  ---
  
  