<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>

CC BY-SA 4.0
2019-08-20T18:02:10.030Z
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?
Kamil S Jaron
CC BY-SA 4.0
2019-08-20T19:19:16.973Z
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.
Ram RS
<r><heatmap>
Argument stopped working
# Argument stopped working

(Asked by: username_0 on 2019-08-20)

I am using ComplexHeatmap 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 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?  
> **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 @KamilSJaron is talking about.  

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## 0 answers

