In case this was a compatability error, I have re-downloaded Rstudio (v1.3) and EnhancedVolcano from:
if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') BiocManager::install('EnhancedVolcano')
But still encounter the same error.
pointSize, labSize, are not autocompleting when typing the condition in my EnhancedVolcano script, which leads me to believe it is not recognized in my package.
DrawConnectors autocompletes, but when used does not generate a plot (plot window in Rstudio is completely blank).
If I do not include
labSize, the plot generates, but when included I lose the plot
Error in EnhancedVolcano(df1, lab = row.names(df1), x = "log2FC", y = "Age.Adjusted.FDR", : unused arguments (pointSize = c(ifelse(df1$log2FC > 0.3, 8, 1)), drawConnectors = TRUE) EnhancedVolcano(df1, lab = row.names(df1), x = "log2FC", y = "Age.Adjusted.FDR", ylab = bquote(~-Log~italic(FDR)), title = "Volcano Plot", pCutoff = 0.2, FCcutoff = 0.3, legendPosition = "right", pointSize = c(ifelse(df1$log2FC > 0.3, 8, 1)), labSize = 4.0, col=c("black", "orange", "blue", "red"), legend=c("NS","Log2 FC > |0.3|","FDR < 0.2","FDR < 0.2 & Log2 FC > |0.3|"), drawConnectors = TRUE, ylim = c(0,-log10(10e-4)) )
Is there an obvious reason I'm missing as to why these lines aren't working? Or an alternative method to increase the point size and label size of specific genes?