text: user285: Im trying to plot reactome pathway in for of circular bar plot using ggplot2 
  my data
      dput(df2)
  structure(list(ID = 1:10, Pathway_names = structure(c(5L, 1L, 
  7L, 6L, 2L, 3L, 9L, 8L, 10L, 4L), .Label = c("Antigen Presentation: Folding assembly and peptide loading of class I MHC", 
  "Antigen processing-Cross presentation", "Class I MHC mediated antigen processing & presentation", 
  "Cytokine Signaling in Immune system", "Endosomal/Vacuolar pathway", 
  "ER-Phagosome pathway", "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell", 
  "Interferon alpha/beta signaling", "Interferon gamma signaling", 
  "Interferon Signaling"), class = "factor"), Entities_found = structure(c(1L, 
  2L, 3L, 4L, 4L, 5L, 6L, 7L, 8L, 9L), .Label = c("51", "54", "55", 
  "57", "75", "77", "96", "117", "176"), class = "factor"), Entities_pValue = c(1.11e-16, 
  1.11e-16, 0.003908431, 2.54e-12, 2.77e-10, 0.0053068, 1.64e-13, 
  1.11e-16, 1.11e-16, 3.68e-06)), row.names = c(NA, -10L), class = "data.frame")
  
  my code 
  ggplot(df2, aes(x = factor(Pathway_names), y = Entities_found)) + ######################################
    geom_bar(aes(fill = Entities_pValue), stat = "identity", position = "stack") + 
    #scale_fill_manual(values = c(blank = "white", dark = "black")) + 
    coord_polar() + 
    theme_minimal() + 
    guides(fill = FALSE)
  
  
  So far im not sure how to include both p value and entities in the plot so that the pathway that are coming up can be labeled accordingly 
  New figure 
  
  user1855: The adjustcolor function from grDevices can be used to generate colours with transparency. What you want is colours based on the pathway and transparency to form a colour gradient for the p-value.
  adjustcolor( "red", alpha.f = 0.2)
  For the ggplot example, the aes function has an alpha parameter.
  ggplot(df2, aes(x = factor(Pathway_names), y = Entities_found), alpha = Entities_pValue) + ######################################
  geom_bar(aes(fill = Entities_found, alpha = Entities_pValue), stat = "identity", position = "stack") +  
  coord_polar() + 
  theme_minimal() + 
   guides(fill = FALSE)
  
  
original_text: 285: <p>Im trying to plot reactome pathway in for of circular bar plot using ggplot2 </p>
  
  <p>my data</p>
  
  <pre><code>    dput(df2)
  structure(list(ID = 1:10, Pathway_names = structure(c(5L, 1L, 
  7L, 6L, 2L, 3L, 9L, 8L, 10L, 4L), .Label = c("Antigen Presentation: Folding assembly and peptide loading of class I MHC", 
  "Antigen processing-Cross presentation", "Class I MHC mediated antigen processing &amp; presentation", 
  "Cytokine Signaling in Immune system", "Endosomal/Vacuolar pathway", 
  "ER-Phagosome pathway", "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell", 
  "Interferon alpha/beta signaling", "Interferon gamma signaling", 
  "Interferon Signaling"), class = "factor"), Entities_found = structure(c(1L, 
  2L, 3L, 4L, 4L, 5L, 6L, 7L, 8L, 9L), .Label = c("51", "54", "55", 
  "57", "75", "77", "96", "117", "176"), class = "factor"), Entities_pValue = c(1.11e-16, 
  1.11e-16, 0.003908431, 2.54e-12, 2.77e-10, 0.0053068, 1.64e-13, 
  1.11e-16, 1.11e-16, 3.68e-06)), row.names = c(NA, -10L), class = "data.frame")
  </code></pre>
  
  <p>my code </p>
  
  <pre><code>ggplot(df2, aes(x = factor(Pathway_names), y = Entities_found)) + ######################################
    geom_bar(aes(fill = Entities_pValue), stat = "identity", position = "stack") + 
    #scale_fill_manual(values = c(blank = "white", dark = "black")) + 
    coord_polar() + 
    theme_minimal() + 
    guides(fill = FALSE)
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/ohhY1.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/ohhY1.jpg" alt="my output "></a></p>
  
  <p>So far im not sure how to include both p value and entities in the plot so that the pathway that are coming up can be labeled accordingly </p>
  
  <p>New figure <a href="https://i.stack.imgur.com/pZjL9.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/pZjL9.jpg" alt="updated figure"></a></p>
   1855: <p>The <code>adjustcolor</code> function from <code>grDevices</code> can be used to generate colours with transparency. What you want is colours based on the pathway and transparency to form a colour gradient for the p-value.</p>
  
  <p><code>adjustcolor( "red", alpha.f = 0.2)</code></p>
  
  <p>For the ggplot example, the <code>aes</code> function has an <code>alpha</code> parameter.</p>
  
  <pre><code>ggplot(df2, aes(x = factor(Pathway_names), y = Entities_found), alpha = Entities_pValue) + ######################################
  geom_bar(aes(fill = Entities_found, alpha = Entities_pValue), stat = "identity", position = "stack") +  
  coord_polar() + 
  theme_minimal() + 
   guides(fill = FALSE)
  </code></pre>
  