text: user4595: I want to have a plot violin plot around quasirandom dots - like below
  
  This is my data
  > str(long1)
  Classes ‘data.table’ and 'data.frame':  116 obs. of  4 variables:
   $ gene    : chr  "WT1" "KRT7" "MUC16" "EPCAM" ...
   $ variable: chr  "1016" "1016" "1016" "1016" ...
   $ value   : num  5.82 8.41 11.22 7.21 5.4 ...
   $ group   : chr  "Tumour" "Tumour" "Tumour" "Tumour" ...
   - attr(*, ".internal.selfref")=<externalptr> 
  >
  
  By this code I get plot which does not have any violin
  library(ggplot2)
  library(ggpubr)
  library(ggbeeswarm)
  p <- ggplot(long1, aes(x=group, y=value,fill=group))
  p +geom_quasirandom(method = 'quasirandom',alpha = 0.2, width = 0.2,aes(colour = variable))+ labs(title="Supplementary Figure 6B", y = "Expression(logcounts)")+theme_classic()+
    theme(legend.position="right") +
    theme(legend.title=element_blank())+facet_wrap(~gene, scales = "free")+theme(strip.background = element_blank(),strip.text.x = element_text(size = 12,face="italic"))
  
  
  I also tried adding geom_violin like
  p <- ggplot(long1, aes(x=group, y=value,fill=group))
  p +geom_violin()+geom_quasirandom(method = 'quasirandom',alpha = 0.2, width = 0.2,aes(colour = variable))+ labs(title="Supplementary Figure 6B", y = "Expression(logcounts)")+theme_classic()+
    theme(legend.position="right") +
    theme(legend.title=element_blank())+facet_wrap(~gene, scales = "free")+theme(strip.background = element_blank(),strip.text.x = element_text(size = 12,face="italic"))
  
  But gives a weird plot not similar to what I want
  
  Any help please
  EDITED
  Thanks to @haci
  By this code I get this plot but as you see the point color inside the violin is not really similar to what I want
  Any suggestion to get a similar color scheme for dots inside the violins
  p <- ggplot(long1, aes(x=group, y=value,fill=group))+guides(fill = "none")
  p +geom_violin(alpha = 0.1)+scale_fill_manual(values=c("#fcf4e0", "#fcf4e0"))+geom_quasirandom(method = 'quasirandom',alpha = 0.2, width = 0.2,size=2,stroke=0.5,aes(colour = variable))+scale_color_hue(l = 5, c = 150)+ labs(title="Supplementary Figure 6B", y = "Expression(logcounts)")+theme_classic()+
    theme(legend.position="right",legend.text=element_text(size=12)) +
    theme(legend.title=element_blank(),legend.text.align = 0,text = element_text(family = "Arial"),
          axis.title.x = element_text(size = 0.00001),
          axis.title.y = element_text(size = 17))+theme(axis.text = element_text(
            color="black", 
            size=12, 
            face=1)
          )+facet_wrap(~gene, scales = "free")+theme(strip.background = element_blank(),strip.text.x = element_text(size = 17,face="italic"))+ theme(axis.line = element_line(colour = 'black', size = 0.8))
  
  
  
  user3541: You are almost there, if you set the alpha parameter within your geom_violin() call (to sth like 0.1) you should be able to get a plot similar to the example plot.
  The fact that you only have two data points for the Stroma group and these two points having similar values, you will end up getting a horizontal-line like violin for this group. Moreover, you do not have that many data points in general anyway so you might consider not using violins at all, especially if the outliers in Tumour group is coming from the same (maybe somewhat problematic?) sample, that might need to be dropped from the analysis. The reader should be able to grasp the essence of the data with our without violins (violins could help making the outliers obvious though).
  
original_text: 4595: <p>I want to have a plot violin plot around quasirandom dots - like below</p>
  <p><a href="https://i.stack.imgur.com/9EXRz.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/9EXRz.png" alt="enter image description here" /></a></p>
  <p>This is my data</p>
  <pre><code>&gt; str(long1)
  Classes ‘data.table’ and 'data.frame':  116 obs. of  4 variables:
   <span class="math-container">$ gene    : chr  "WT1" "KRT7" "MUC16" "EPCAM" ...
   $</span> variable: chr  &quot;1016&quot; &quot;1016&quot; &quot;1016&quot; &quot;1016&quot; ...
   <span class="math-container">$ value   : num  5.82 8.41 11.22 7.21 5.4 ...
   $</span> group   : chr  &quot;Tumour&quot; &quot;Tumour&quot; &quot;Tumour&quot; &quot;Tumour&quot; ...
   - attr(*, &quot;.internal.selfref&quot;)=&lt;externalptr&gt; 
  &gt;
  </code></pre>
  <p>By this code I get plot which does not have any violin</p>
  <pre><code>library(ggplot2)
  library(ggpubr)
  library(ggbeeswarm)
  p &lt;- ggplot(long1, aes(x=group, y=value,fill=group))
  p +geom_quasirandom(method = 'quasirandom',alpha = 0.2, width = 0.2,aes(colour = variable))+ labs(title=&quot;Supplementary Figure 6B&quot;, y = &quot;Expression(logcounts)&quot;)+theme_classic()+
    theme(legend.position=&quot;right&quot;) +
    theme(legend.title=element_blank())+facet_wrap(~gene, scales = &quot;free&quot;)+theme(strip.background = element_blank(),strip.text.x = element_text(size = 12,face=&quot;italic&quot;))
  </code></pre>
  <p><a href="https://i.stack.imgur.com/jzkyP.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/jzkyP.png" alt="enter image description here" /></a></p>
  <p>I also tried adding geom_violin like</p>
  <pre><code>p &lt;- ggplot(long1, aes(x=group, y=value,fill=group))
  p +geom_violin()+geom_quasirandom(method = 'quasirandom',alpha = 0.2, width = 0.2,aes(colour = variable))+ labs(title=&quot;Supplementary Figure 6B&quot;, y = &quot;Expression(logcounts)&quot;)+theme_classic()+
    theme(legend.position=&quot;right&quot;) +
    theme(legend.title=element_blank())+facet_wrap(~gene, scales = &quot;free&quot;)+theme(strip.background = element_blank(),strip.text.x = element_text(size = 12,face=&quot;italic&quot;))
  </code></pre>
  <p>But gives a weird plot not similar to what I want</p>
  <p><a href="https://i.stack.imgur.com/kVc4e.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/kVc4e.png" alt="enter image description here" /></a></p>
  <p>Any help please</p>
  <p><em><strong>EDITED</strong></em></p>
  <p>Thanks to @haci</p>
  <p>By this code I get this plot but as you see the point color inside the violin is not really similar to what I want</p>
  <p>Any suggestion to get a similar color scheme for dots inside the violins</p>
  <pre><code>p &lt;- ggplot(long1, aes(x=group, y=value,fill=group))+guides(fill = &quot;none&quot;)
  p +geom_violin(alpha = 0.1)+scale_fill_manual(values=c(&quot;#fcf4e0&quot;, &quot;#fcf4e0&quot;))+geom_quasirandom(method = 'quasirandom',alpha = 0.2, width = 0.2,size=2,stroke=0.5,aes(colour = variable))+scale_color_hue(l = 5, c = 150)+ labs(title=&quot;Supplementary Figure 6B&quot;, y = &quot;Expression(logcounts)&quot;)+theme_classic()+
    theme(legend.position=&quot;right&quot;,legend.text=element_text(size=12)) +
    theme(legend.title=element_blank(),legend.text.align = 0,text = element_text(family = &quot;Arial&quot;),
          axis.title.x = element_text(size = 0.00001),
          axis.title.y = element_text(size = 17))+theme(axis.text = element_text(
            color=&quot;black&quot;, 
            size=12, 
            face=1)
          )+facet_wrap(~gene, scales = &quot;free&quot;)+theme(strip.background = element_blank(),strip.text.x = element_text(size = 17,face=&quot;italic&quot;))+ theme(axis.line = element_line(colour = 'black', size = 0.8))
  </code></pre>
  <p><a href="https://i.stack.imgur.com/siY8V.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/siY8V.png" alt="enter image description here" /></a></p>
   3541: <p>You are almost there, if you set the <code>alpha</code> parameter within your <code>geom_violin()</code> call (to sth like 0.1) you should be able to get a plot similar to the example plot.</p>
  <p>The fact that you only have two data points for the <code>Stroma</code> group and these two points having similar values, you will end up getting a horizontal-line like violin for this group. Moreover, you do not have that many data points in general anyway so you might consider not using violins at all, especially if the outliers in <code>Tumour</code> group is coming from the same (maybe somewhat problematic?) sample, that might need to be dropped from the analysis. The reader should be able to grasp the essence of the data with our without violins (violins could help making the outliers obvious though).</p>
  