Print EnhancedVolcano Plot as jpeg or similar in R Notebook
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Bine ▴ 20
@bine-23912
Last seen 22 days ago
UK

Dear all,

I have created an enhancedvolcano plot, which worked perfectly. But now i am struggling a bit to save it as an image in a R Notebook.

Can anyone advise me how to do it?

I tried right click and download or copy image but it doesnt work.

Thanks so much!

EnhancedVolcano • 187 views
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@kevin
Last seen 1 hour ago
Republic of Ireland

Hi, I am the main developer of EnhancedVolcano. This question seems unrelated to any technical issue pertaining to the package. Irrespective, can you show me the code chunk from your markdown where you are trying to generate the plot?

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I am trying to save this plot to a jpeg or similar:

EnhancedVolcano(top_volcano,
                lab = top_volcano$gene,
                x = 'log2FoldChange',
                y = 'pvalue',
                title = 'Differential Expression Analysis',
                subtitle = "test",
                pCutoff =10e-7 ,
                FCcutoff = 1.2,
                pointSize = 3.0,
                labSize = 6.0)

Thank you!!

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Hi, you just need the jpeg() function, for example:

jpeg('EV.jpg')
  EnhancedVolcano(top_volcano,
                lab = top_volcano$gene,
                x = 'log2FoldChange',
                y = 'pvalue',
                title = 'Differential Expression Analysis',
                subtitle = "test",
                pCutoff =10e-7 ,
                FCcutoff = 1.2,
                pointSize = 3.0,
                labSize = 6.0)
dev.off()

Depending on the situation, you may need the following:

jpeg('EV.jpg')
  print(EnhancedVolcano(top_volcano,
                lab = top_volcano$gene,
                x = 'log2FoldChange',
                y = 'pvalue',
                title = 'Differential Expression Analysis',
                subtitle = "test",
                pCutoff =10e-7 ,
                FCcutoff = 1.2,
                pointSize = 3.0,
                labSize = 6.0))
dev.off()

Also take a look at ggsave()

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Thank you. The jpg it creates this way is empty. Remember I am doing it in R Notebook. But it did work with ggsave().

Many thanks

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Great! problem solved, then?

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