Answers.Body: <p><a href="https://github.com/satijalab/seurat/issues/287" rel="nofollow noreferrer">https://github.com/satijalab/seurat/issues/287</a></p>
  
  <p>In this post there is a answer for my question, however when I set scale to FALSE again the number of genes did not change but the shape of plot dramatically changed. So, maybe the issue is because of scaling that did not solve my problem</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-22T07:26:29.817Z
Answers.LastActivityDate: 2018-08-22T07:26:29.817Z
Answers.UserDisplayName: Zizogolu
Body: <p>I am heatmaping a list of genes by DoHeatmap function in Seurat R package. I am sure I have 212 genes but heat map shows only a few of my genes</p>
  
  <pre><code>&gt; DoHeatmap(
  +        object = seurat,
  +        genes.use = genes,
  +        slim.col.label = TRUE, 
  +        remove.key = TRUE)
  &gt; dim(as.matrix(seurat@data))
  [1] 12293   209
  
  &gt; length(genes)
  [1] 212
  &gt; class(genes)
  [1] "character"
  
  &gt; class(seurat)
  [1] "seurat"
  attr(,"package")
  [1] "Seurat"
  &gt; 
  </code></pre>
  
  <p>Please look at heat map, I was trying to plot 212 genes but you seeing only few genes are among my 212 genes</p>
  
  <p>Please somebody save me from this confusion</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-21T16:33:55.597Z
Comments.Text: This is probably a very naive question, but do more genes appear if you make the image larger? I mean, if you extend the image before exporting it, while it is being displayed in R?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-21T16:34:44.427Z
Comments.Text: Actually no, because before exporting from R looks the same :(
Comments.UserDisplayName: Zizogolu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-21T16:36:33.263Z
Comments.Text: Yes, but what if you resize it before exporting? Does making the image bigger make more genes appear? I just want to rule out the obvious here.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-21T16:48:29.590Z
Comments.Text: Thank you, I just change the size of image before exposing to 2500*1991 but only rows became smaller and the order and number of genes are the same
Comments.UserDisplayName: Zizogolu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-21T16:54:27.990Z
Comments.Text: Oh well. It was not very likely to be that simple.
Comments.UserDisplayName: terdon
Tags: <r><scrnaseq><seurat>
Title: Why DoHeatmap Does not show all genes in genes.use?
ThreadText: # Why DoHeatmap Does not show all genes in genes.use?
  
  (Asked by: username_0 on 2018-08-21)
  
  I am heatmaping a list of genes by DoHeatmap function in Seurat R package. I am sure I have 212 genes but heat map shows only a few of my genes
  
  ```
  > DoHeatmap(
  +        object = seurat,
  +        genes.use = genes,
  +        slim.col.label = TRUE, 
  +        remove.key = TRUE)
  > dim(as.matrix(seurat@data))
  [1] 12293   209
  
  > length(genes)
  [1] 212
  > class(genes)
  [1] "character"
  
  > class(seurat)
  [1] "seurat"
  attr(,"package")
  [1] "Seurat"
  > 
  
  ```
  
  Please look at heat map, I was trying to plot 212 genes but you seeing only few genes are among my 212 genes
  
  Please somebody save me from this confusion
  
  **Tags:** r, scrnaseq, seurat
  
  > **Comments:**
  > **username_1**: This is probably a very naive question, but do more genes appear if you make the image larger? I mean, if you extend the image before exporting it, while it is being displayed in R?  
  > **username_0**: Actually no, because before exporting from R looks the same :(  
  > **username_1**: Yes, but what if you resize it before exporting? Does making the image bigger make more genes appear? I just want to rule out the obvious here.  
  > **username_0**: Thank you, I just change the size of image before exposing to 2500*1991 but only rows became smaller and the order and number of genes are the same  
  > **username_1**: Oh well. It was not very likely to be that simple.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-08-22. Score: 1 | Accepted answer
  
  <https://github.com/satijalab/seurat/issues/287>
  
  In this post there is a answer for my question, however when I set scale to FALSE again the number of genes did not change but the shape of plot dramatically changed. So, maybe the issue is because of scaling that did not solve my problem
  
  
  ---
  
  