How to plot volcano plots without getting the not numeric error

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!

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:

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.

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.

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