Error in Enhanced Volcano : unused arguments

Question

[Michael]

Hi all,

So I am currently attempting to use Enhanced volcano to visualise a set of RNA-seq data, but when I run the below script, I get back the error message below. Does anyone know what the problem is - I can't see anything wrong in the code.

Error in EnhancedVolcano(RV16_byweights, lab = RV16_byweights$SYMBOL,  : 
  unused arguments (pCutoffCol = "adj.P.Val", max.overlaps = Inf, maxoverlapsConnectors = 50)

My File is labelled - RV16_byweights

Head of file:

My code:

EnhancedVolcano(RV16_byweights, #dataframe
            lab = RV16_byweights$SYMBOL, #gene symbol for labels
            x='logFC', y='P.Value', #values for axis
            title='RV16 Volcano plot', 
            subtitle='With Quality Weights',
            pCutoffCol = 'adj.P.Val', #use adjusted p value for cutoff value 
            pCutoff = 0.05, FCcutoff=0.5, #cutoff lines for graph 
            ylim = c(0, 10), #axis limits
            xlim = c(-2, 4),
            pointSize=2, labSize=3, #point and label size
            colCustom = keyvals2, #custom colours set up above
            colAlpha = 5,
            legendPosition = 'bottom',
            legendLabSize = 10,
            legendIconSize = 5,
            axisLabSize = 10,
            xlab = 'LogFC', 
            drawConnectors = TRUE, #lines from labels to dots
            widthConnectors = 0.25, #width of connectors
            max.overlaps = 20,
            maxoverlapsConnectors = 50, #max number of overlaps allowed
            colConnectors = 'black', 
            boxedLabels = FALSE, #box around labels 
            arrowheads = FALSE, 
            gridlines.major = TRUE,
            gridlines.minor = FALSE,
            border = 'full',
            borderWidth = 1,
            borderColour = 'black',
            )

[jared.andrews07]

The dev has made it clear that he'd prefer such questions were posted on the Bioconductor support site. If you post it there, he'll likely be able to help you out.

Answer 1

[ATpoint]

Try upgrading the package. It was added relatively recently https://github.com/kevinblighe/EnhancedVolcano/commit/fc46969083a8ae24084ecf98cba3d464a855ac4f#diff-8c2574892063f995fdf756bce07f46c1a5193e54cd52837ed91e32008ccf41ac

[Michael]

Thank you - for some reason, even though I am running the latest R Studio it was still installing an older version (I installed it this morning)

As a workaround i found the following helped

remove.packages('EnhancedVolcano')

Restart R.

devtools::install_github('kevinblighe/EnhancedVolcano')

Works like a charm now