Body: <p>I am using <a href="https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html" rel="nofollow noreferrer">ComplexHeatmap</a> package for transcriptomic analyses and all of a sudden,  <code>row_labels</code> and <code>column_labels</code> as well as <code>heatmap_width</code> and <code>heatmap_height</code> stopped being recognized as arguments of the function Heatmap:</p>
  
  <p>actual Heatmap</p>
  
  <pre><code>Heatmap(matrix [RowFunctionOrder,ColumnImposedOrder],
          col = colgrad,
          show_column_names = F,
          cluster_columns = FALSE,
          cluster_rows = FALSE,
          row_names_gp = gpar(fontsize=7),
          heatmap_width=1,
          heatmap_height = 1, 
          row_labels =  rnaseqMatrix$Protein.ID,
          bottom_annotation = Column_ha
          )
  #creating a column annotation
  
  Column_ha = HeatmapAnnotation(condition = colnames(matrix),condition = runif(30), col = list(condition=Colcolour), show_legend = FALSE).
  
  
  *Error in Heatmap(matrix[RowFunctionOrder, ColumnImposedOrder], col = colgrad,  : 
    unused arguments (heatmap_width = 1, heatmap_height = 1, row_labels = rnaseqMatrix$Protein.ID)*.
  </code></pre>
  
  <p>this code was perfectly working this morning, I do not understand why suddenly the arguments were not valid anymore. they also seem to have disappeared from the help menu. this event followed a bug where I was receiving messaged saying the <code>help(ComplexHeatmap) could't be update.</code> this messages started appearing when I started typing arguments.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-20T18:02:10.030Z
Comments.Text: Hello Jordan, my best guess is that you have loaded a different package that has masked the original `Heatmap` function from `ComplexHeatmap` package. Does you have the same problem when you start a new R session and load only `ComplexHeatmap` package?
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-20T19:19:16.973Z
Comments.Text: Please edit your question and add the output of `sessionInfo()`. Also, try using `ComplexHeatmap::Heatmap()` instead of just `Heatmap()` - that should tell you if you're running into what @KamilSJaron is talking about.
Comments.UserDisplayName: Ram RS
Tags: <r><heatmap>
Title: Argument stopped working
ThreadText: # Argument stopped working
  
  (Asked by: username_0 on 2019-08-20)
  
  I am using [ComplexHeatmap](https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html) package for transcriptomic analyses and all of a sudden, `row_labels` and `column_labels` as well as `heatmap_width` and `heatmap_height` stopped being recognized as arguments of the function Heatmap:
  
  actual Heatmap
  
  ```
  Heatmap(matrix [RowFunctionOrder,ColumnImposedOrder],
          col = colgrad,
          show_column_names = F,
          cluster_columns = FALSE,
          cluster_rows = FALSE,
          row_names_gp = gpar(fontsize=7),
          heatmap_width=1,
          heatmap_height = 1, 
          row_labels =  rnaseqMatrix$Protein.ID,
          bottom_annotation = Column_ha
          )
  #creating a column annotation
  
  Column_ha = HeatmapAnnotation(condition = colnames(matrix),condition = runif(30), col = list(condition=Colcolour), show_legend = FALSE).
  
  *Error in Heatmap(matrix[RowFunctionOrder, ColumnImposedOrder], col = colgrad,  : 
    unused arguments (heatmap_width = 1, heatmap_height = 1, row_labels = rnaseqMatrix$Protein.ID)*.
  
  ```
  
  this code was perfectly working this morning, I do not understand why suddenly the arguments were not valid anymore. they also seem to have disappeared from the help menu. this event followed a bug where I was receiving messaged saying the `help(ComplexHeatmap) could't be update.` this messages started appearing when I started typing arguments.
  
  **Tags:** r, heatmap
  
  > **Comments:**
  > **username_1**: Hello username_0, my best guess is that you have loaded a different package that has masked the original `Heatmap` function from `ComplexHeatmap` package. Does you have the same problem when you start a new R session and load only `ComplexHeatmap` package?  
  > **username_2**: Please edit your question and add the output of `sessionInfo()`. Also, try using `ComplexHeatmap::Heatmap()` instead of just `Heatmap()` - that should tell you if you're running into what @username_1 is talking about.  
  
  ---
  
  ## 0 answers
  
  