Hi, I have DEGs file (DEAdf) with log2FC and padjust. I am trying to look at significant dowreguated and upregulated genes in enhanced volcano plot according to my cutoff. To visulize the up and down regulated genes, I customized them into different colors (keyvals.colour), but somehow it came out with the error like the title (Error: Aesthetics must be either length 1 or the same as the data (): colour ) Can anyone help with the solution? many thanks. ( normally, the enhanced volcano plot like this)
library(EnhancedVolcano) mypval=0.05 myfc=2 mypadj=0.05 mylog2fc=log2(myfc)
keyvals.colour <- ifelse( DEAdf$log2FC < -1 & DEAdf$padjust<0.05, 'royalblue', ifelse(DEAdf$log2FC > 1 & DEAdf$padjust<0.05,'red2', ifelse(DEAdf$log2FC<=1 & DEAdf$log2FC >= -1 & DEAdf$padjust >= 0.05,"forestgreen", ifelse(DEAdf$log2FC<=1 & DEAdf$log2FC >=-1 & DEAdf$padjust < 0.05,"yellow", 'grey30'))))
EnhancedVolcano(DEAdf, lab = DEAdf, x = 'log2FC', y = 'padjust', xlim = c(min(DEAdf$log2FC, na.rm=TRUE), max(DEAdf$log2FC, na.rm=TRUE)), ylim=c(0, max(-log10(DEAdf$padjust), na.rm=TRUE) + 1), title="samples", pCutoff=mypadj, FCcutoff=mylog2fc, pointSize = 2.0, labSize = 3.0, colCustom = keyvals.colour, colAlpha = 1, xlab = bquote(~Log[2]~ 'fold change'), ylab = bquote(~-Log[10]~adjusted~italic(P)), legend=c('No significant','Log2FC','Adjusted p-value', 'Adjusted p-value & Log2FC<-1','Adjusted p-value & Log2FC>1'), col=c("grey30", "forestgreen", "Yellow", "royalblue","red2"), legendPosition = 'top', legendLabSize = 10, legendIconSize = 5.0, widthConnectors = 0.2, colConnectors = 'grey30') dev.off()
