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lijingya / ELMER

Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes
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Error in heatmapPairs in ELMER #19

Open Rahel14350 opened 5 years ago

Rahel14350 commented 5 years ago

Dear @tiagochst I have this error in the last step of ELMER package. I have list of pair genes and I would plot them with heatmapPairs but I have this error. Can you please help me here:

> heatmapPairs(data = mae, 
+              group.col = "gene2",
+              group1 = "low", 
+              annotation.col = c("gene2", "exprs_rank"),
+              group2 = "high",
+              pairs = pair,
+              filename =  "heatmap.meth_expression.primary.results.pdf")
Ordering groups
Error in splitter_a(.data, .margins, .expand) : Invalid margin

Many thanks in advance, Rahel

tiagochst commented 5 years ago

I would need to have the object to debug this problem. Please, is it possible to share it?

Em 11 de fev de 2019, à(s) 07:39, RahelSh notifications@github.com escreveu:

Dear @tiagochst I have this error in the last step of ELMER package. I have list of pair genesand I would plot them with heatmapPairs but I have this error. Can you please help me here:

heatmapPairs(data = mae,

  • group.col = "gene2",
  • group1 = "low",
  • annotation.col = c("gene2", "exprs_rank"),
  • group2 = "high",
  • pairs = pair,
  • filename = "heatmap.meth_expression.primary.results.pdf") Ordering groups Error in splitter_a(.data, .margins, .expand) : Invalid margin

Many thanks in advance, Rahel

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Rahel14350 commented 5 years ago

Yes, sure it is fine. Which file should I send to you?

tiagochst commented 5 years ago

I would need the mae and pair objects saved as an rda.

Em 11 de fev de 2019, à(s) 08:23, RahelSh notifications@github.com escreveu:

Yes, sure it is fine. Which file should I send to you?

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Rahel14350 commented 5 years ago

Dear Tiago, I could solve the problem, I was using a column from "mae" which it was a factor and when I changed to Character, the error was gone and I could get the heatmap. Many many thanks for your reply and help, Rahel