How to plot volcano plots without getting the not numeric error

tidyverse
#1

Hi,

I'm trying to create a volcano plot and keep getting the same error.

I ran the following code in RStudio...

EnhancedVolcano(res, lab = rownames(res), x = 'Log2foldchange', y = 'pvalue', xlim = c(-8,8), title = 'Macrophage', pCutoff = 10e-16, FCcutoff = 1.5, pointSize = 3.0, labSize = 3.0)

And received the following error...

Error in EnhancedVolcano(toptable = data.frame(results), x = "log2fc", : log2fc is not numeric!

#2

Hi, welcome!

To help us help you, could you please prepare a reproducible example (reprex) illustrating your issue? Please have a look at this guide, to see how to create one:

#3

I tried to downloading "datapasta" and received the following issues,

Warning in install.packages :
installation of package ‘readr’ had non-zero exit status
ERROR: dependency ‘readr’ is not available for package ‘datapasta’

  • removing ‘/home/piquemi1/R/x86_64-pc-linux-gnu-library/3.6/datapasta’
    Warning in install.packages :
    installation of package ‘datapasta’ had non-zero exit status

not sure how to add the data file.

#4

I tried to downloading "datapasta" and received the following issues,

Warning in install.packages :
installation of package ‘readr’ had non-zero exit status
ERROR: dependency ‘readr’ is not available for package ‘datapasta’

  • removing ‘/home/piquemi1/R/x86_64-pc-linux-gnu-library/3.6/datapasta’
    Warning in install.packages :
    installation of package ‘datapasta’ had non-zero exit status

not sure how to add the data file.

#5

This is telling you that you have to install readr first, but regardless, you could still use dput() function without installing anything.

#6

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