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JoachimGoedhart / VolcaNoseR

Shiny app for making and annotating Volcano plots
https://huygens.science.uva.nl/VolcaNoseR/
GNU General Public License v3.0
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Inverted volcano plot #9

Closed etiennedanis closed 3 years ago

etiennedanis commented 3 years ago

Hi Joachim, I am getting a volcano plot but it is inverted: Instead of looking like a V, it looks like an A. I got normal volcano/V shape doing volcano plots with ggplot2 or EnhancedVolcano with my data set. Is there any option I should select or unselect? Also, is there an option to select a specific adjusted p-value? Thank you very much in advance. Best, Etienne

JoachimGoedhart commented 3 years ago

That's weird - did you select the right columns for plotting? You can send me the data by email and I'd be happy to take a look! Cheers, Joachim.

On Mar 9, 2021, at 18:33 , Etienne Danis notifications@github.com wrote:

Hi Joachim, I am getting a volcano plot but it is inverted: Instead of looking like a V, it looks like an A. I got normal volcano/V shape doing volcano plots with ggplot2 or EnhancedVolcano with my data set. Is there any option I should select or unselect? Also, is there an option to select a specific adjusted p-value? Thank you very much in advance. Best, Etienne

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farhan-lab commented 12 months ago

Hi,

I have the same issue of the inverted plots. Could you share what right columns should be plotted? I have used the X column as fold change and for Y axis, I select P value, but my volcano plot is inverted.

Thanks, Farhan

JoachimGoedhart commented 11 months ago

Please note that the app only plots the data and does no processing. From what I understand, you plot p-values, but the standard Volcano plot uses -log[p-value].

I hope this helps. If not, you could send me the data by email and I'd be happy to take a look! Cheers, Joachim.