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Error in superheat: #61

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dcpattie opened this issue Dec 13, 2018 · 3 comments

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commented Dec 13, 2018

Hello, I'm following your excellent biomarker pipeline and ran across an error with the heatmap/dendrogram command (see below).

heatmap_ic(x = limmaTMLEout,
+            row.dendrogram = TRUE,
+            clustering.method = "hierarchical",
+            design = design, FDRcutoff = 1.0, top = 10)
**Error in superheat::superheat(as.matrix(biomarkerTMLEout_top), row.dendrogram = TRUE,  : 
  formal argument "row.dendrogram" matched by multiple actual arguments**

I installed the superheat package so I'm not sure where the error is coming from?

@nhejazi nhejazi self-assigned this Dec 13, 2018

@nhejazi nhejazi added the bug label Dec 13, 2018

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commented Dec 13, 2018

Thanks for reporting this. Just a few clarifications: What versions of the superheat and biotmle are being used in the example? (e.g., CRAN installation of superheat v0.1.0; Bioconductor 3.8 installation of biotmle v1.6.0). I recall seeing this bug myself at some point during testing but thought it had been resolved on the version of biotmle on the master branch.

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commented Dec 13, 2018

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commented Dec 17, 2018

After replacing the development version of biotmle with v1.6.0 from Bioconductor v3.8, I've been able to replicate this behavior. Please note that this is not technically a bug in either biotmle or superheat but due to a change in the heatmap_ic function. Note that the version of the function in v1.6.0 (here) of the package forces the argument row.dendrogram = TRUE in its call to superheat; however, in the development version (here), that setting has been removed, making it so that row.dendrogram = TRUE must be manually passed to superheat via heatmap_ic.

The easiest way to repair this, while still using v1.6.0 of biotmle from Bioconductor v3.8, would be to amend your example as follows

heatmap_ic(x = limmaTMLEout,
+            clustering.method = "hierarchical",
+            design = design, FDRcutoff = 1.0, top = 10)

I'm going to go ahead and close this issue but feel free to re-open should the problem persist.

@nhejazi nhejazi closed this Dec 17, 2018

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