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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

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  • 1
    $\begingroup$ 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? $\endgroup$
    – terdon
    Aug 21 '18 at 16:33
  • $\begingroup$ Actually no, because before exporting from R looks the same :( $\endgroup$
    – Exhausted
    Aug 21 '18 at 16:34
  • 1
    $\begingroup$ 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. $\endgroup$
    – terdon
    Aug 21 '18 at 16:36
  • $\begingroup$ 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 $\endgroup$
    – Exhausted
    Aug 21 '18 at 16:48
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    $\begingroup$ Oh well. It was not very likely to be that simple. $\endgroup$
    – terdon
    Aug 21 '18 at 16:54
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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

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