Question

Print EnhancedVolcano Plot as jpeg or similar in R Notebook

0

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Bine ▴ 50

@bine-23912

Last seen 6 months 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 • 3.3k views

ADD COMMENT • link updated 2.5 years ago by Kevin Blighe ★ 4.0k • written 2.5 years ago by Bine ▴ 50

score 1 · Accepted Answer · 2022-05-19

1

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Kevin Blighe ★ 4.0k

@kevin

Last seen 14 days 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?

ADD COMMENT • link 2.5 years ago Kevin Blighe ★ 4.0k

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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!!

ADD REPLY • link 2.5 years ago Bine ▴ 50

1

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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()

ADD REPLY • link 2.5 years ago Kevin Blighe ★ 4.0k

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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

ADD REPLY • link 2.5 years ago Bine ▴ 50

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Great! problem solved, then?

ADD REPLY • link 2.5 years ago Kevin Blighe ★ 4.0k