Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-12T06:23:27.910Z
Answers.Text: it looks fine now may be i can tweak it a bit more i will see but i see my Entities_found are still 150 but highest one is 176 why am not getting till 176?
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-13T07:01:40.940Z
Answers.Text: i have a doubt the p value gradient still looks confusing ...can you help me regarding that
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-13T07:39:59.333Z
Answers.Text: Try plotting them on a log-scale?
Answers.UserDisplayName: Tom Kelly ケリー・トム
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-13T09:08:14.820Z
Answers.Text: no i haven;t given that thought may be that would help
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-11T14:36:02.527Z
Answers.LastActivityDate: 2018-12-11T14:36:02.527Z
Answers.UserDisplayName: Tom Kelly ケリー・トム
Body: <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.sstatic.net/ohhY1.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/pZjL9.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/pZjL9.jpg" alt="updated figure"></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-11T07:18:43.027Z
Comments.Text: I don't understand the issue. It looks fine to me.
Comments.UserDisplayName: fridaymeetssunday
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-11T08:57:00.470Z
Comments.Text: What do you mean by entities: the third column of your `df2`? You already have the height for the entities and the color for the p-value. How is this plot not what you expected?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-11T09:39:48.163Z
Comments.Text: yes i tried different ways but this is what i end up with  ,but can you suggest me a way to color it so that it can distinguish p value it color scale_manual ?
Comments.UserDisplayName: kcm
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-11T15:20:58.913Z
Comments.Text: @krushnachChandra Sorry I don't understand your question from the comments. You want to distinguish the p-value with the colors? Or do you want to set a manual scale of colors? If the question is the former, you can try to apply `log10`  to the variable to better distinguish the values. If the later case, I don't understand what is your problem with scale_manual
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-11T17:49:44.087Z
Comments.Text: Can I suggest using acronyms for the entity names in the figure? Like ERPP for ER-Phagosome pathway? This way the text can be placed next to its barplot component and be readable.
Comments.UserDisplayName: conchoecia
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-12T06:19:16.767Z
Comments.Text: okay let me try that
Comments.UserDisplayName: kcm
Tags: <r><visualization><ggplot2>
Title: How to plot p-values in a circular barplot?
ThreadText: # How to plot p-values in a circular barplot?
  
  (Asked by: username_0 on 2018-12-10)
  
  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)
  
  ```
  
  [![my output ](https://i.sstatic.net/ohhY1.jpg)](https://i.sstatic.net/ohhY1.jpg)
  
  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 [![updated figure](https://i.sstatic.net/pZjL9.jpg)](https://i.sstatic.net/pZjL9.jpg)
  
  **Tags:** r, visualization, ggplot2
  
  > **Comments:**
  > **username_1**: I don't understand the issue. It looks fine to me.  
  > **username_2**: What do you mean by entities: the third column of your `df2`? You already have the height for the entities and the color for the p-value. How is this plot not what you expected?  
  > **username_0**: yes i tried different ways but this is what i end up with  ,but can you suggest me a way to color it so that it can distinguish p value it color scale_manual ?  
  > **username_2**: @krushnachChandra Sorry I don't understand your question from the comments. You want to distinguish the p-value with the colors? Or do you want to set a manual scale of colors? If the question is the former, you can try to apply `log10`  to the variable to better distinguish the values. If the later case, I don't understand what is your problem with scale_manual  
  > **username_3**: Can I suggest using acronyms for the entity names in the figure? Like ERPP for ER-Phagosome pathway? This way the text can be placed next to its barplot component and be readable.  
  > **username_0**: okay let me try that  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2018-12-11. Score: 3 | Accepted answer
  
  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)
  
  ```
  
  > **Comments:**
  > **username_0**: it looks fine now may be i can tweak it a bit more i will see but i see my Entities_found are still 150 but highest one is 176 why am not getting till 176?  
  > **username_0**: i have a doubt the p value gradient still looks confusing ...can you help me regarding that  
  > **username_4**: Try plotting them on a log-scale?  
  > **username_0**: no i haven;t given that thought may be that would help  
  
  ---
  
  