Hi all,

I want to use enhancedvolcanoes package to produce volcanoes plot, but the example is so confusing with its input data in 'S4' type, obj oriented. I have been looking for an example that shows simple data format that I need to have before inputing them in and use the package. Nowhere to be found!

I just have an excel sheet with 3 columns: `Gene, log2FoldChange, pvalue`

When input into R as VC_data, can we seen as:
<div>https://www.dropbox.com/s/pq1l38ko1p35e8k/Screen%20Shot%202019-05-19%20at%2011.22.13%20PM.png?dl=0</div>

My code is as following:

    EnhancedVolcano(VC_data,
                    lab = VC_data$Gene,
                    x = 'log2FoldChange',
                    y = 'pvalue',
                    xlim = c(-5, 8))

 I keep getting this error saying that 

    'Error in EnhancedVolcano(VC_data, lab = VC_data$Gene, x = "log2FoldChange",  : 
      log2FoldChange is not numeric!'

When I did `is.numeric(VC_data$log2FoldChange)`, I get true.

I am very frustrated. Please help!
Seems to be an issue with your input being a `tibble`:

    tb <- tibble(log2fc = c(2,3), pval = c(0.01, 0.007))
        
    ## this returns the error you have:
    EnhancedVolcano(toptable = tb, x = 'log2fc', y = 'pval', lab = "foo")
    
    ## this one does it properly:
    EnhancedVolcano(toptable = data.frame(tb), x = 'log2fc', y = 'pval', lab = "foo")

=> Convert `tibble` to `data.frame`


Edit:
The way EnhancedVolcano checks if data are numeric is (source code line 76-78):

    if(!is.numeric(toptable[,x])) {
      stop(paste(x, " is not numeric!", sep=""))
    }

Problem is that e.g. `tb[,1]` does not automatically reduces dimensions to directly access the data but returns:

    > tb[,1]
    # A tibble: 2 x 1
     log2fc
      <dbl>
    1      2
    2      3

whereas:

    tb[,1][[1]]
    [1] 2 3

returns the numeric data.

