Yes, the last two lines contradict each other, specifically padj<0.05 & abs(lfc)>=0.58) and padj<0.05 & abs(lfc)>=-0.59).

I think that you want to colour positive fold-change genes as red, and negative as green? Try this:

par(mar=c(5,5,5,5), cex=1.0, cex.main=1.4, cex.axis=1.4, cex.lab=1.4)
res <- read.csv("volcano.txt", header=TRUE,sep = '\t')
topT <- as.data.frame(res)
head(topT)
with(topT, plot(lfc, -log10(padj), pch=20, main="Volcano plot", cex=1.0, xlab=bquote(~Log[2]~fold~change), ylab=bquote(~-log[10]~P~value)))
with(subset(topT, padj<0.05 & lfc>=0.58), points(lfc, -log10(padj), pch=20, col="red", cex=0.5))
with(subset(topT, padj<0.05 & lfc<=-0.59), points(lfc, -log10(padj), pch=20, col="green", cex=0.5))

Here is the code for data in an EdgeR results table:

EnhancedVolcanoEdgeR <- function(toptable, NominalCutoff, AdjustedCutoff, LabellingCutoff, FCCutoff, main)
{
    toptable$Significance <- "NS"
    toptable$Significance[(abs(toptable$logFC) > FCCutoff)] <- "FC"
    toptable$Significance[(toptable$FDR<AdjustedCutoff)] <- "FDR"
    toptable$Significance[(toptable$FDR<AdjustedCutoff) & (abs(toptable$logFC)>FCCutoff)] <- "FC_FDR"
    table(toptable$Significance)
    toptable$Significance <- factor(toptable$Significance, levels=c("NS", "FC", "FDR", "FC_FDR"))

    plot <- ggplot(toptable, aes(x=logFC, y=-log10(FDR))) +

        #Add points:
        #   Colour based on factors set a few lines up
        #   'alpha' provides gradual shading of colour
        #   Set size of points
        geom_point(aes(color=factor(Significance)), alpha=1/2, size=0.8) +

        #Choose which colours to use; otherwise, ggplot2 choose automatically (order depends on how factors are ordered in toptable$Significance)
        scale_color_manual(values=c(NS="grey30", FC="forestgreen", FDR="royalblue", FC_FDR="red2"), labels=c(NS="NS", FC=paste("LogFC>|", FCCutoff, "|", sep=""), FDR=paste("FDR Q<", AdjustedCutoff, sep=""), FC_FDR=paste("FDR Q<", AdjustedCutoff, " & LogFC>|", FCCutoff, "|", sep=""))) +

        #Set the size of the plotting window
        theme_bw(base_size=24) +

        #Modify various aspects of the plot text and legend
        theme(legend.background=element_rect(),
            plot.title=element_text(angle=0, size=12, face="bold", vjust=1),

            panel.grid.major=element_blank(),   #Remove gridlines
            panel.grid.minor=element_blank(),   #Remove gridlines

            axis.text.x=element_text(angle=0, size=12, vjust=1),
            axis.text.y=element_text(angle=0, size=12, vjust=1),
            axis.title=element_text(size=12),

            #Legend
            legend.position="top",          #Moves the legend to the top of the plot
            legend.key=element_blank(),     #removes the border
            legend.key.size=unit(0.5, "cm"),    #Sets overall area/size of the legend
            legend.text=element_text(size=8),   #Text size
            title=element_text(size=8),     #Title text size
            legend.title=element_blank()) +     #Remove the title

        #Change the size of the icons/symbols in the legend
        guides(colour = guide_legend(override.aes=list(size=2.5))) +

        #Set x- and y-axes labels
        xlab(bquote(~Log[2]~ "fold change")) +
        ylab(bquote(~-Log[10]~adjusted~italic(P))) +

        #Set the axis limits
        #xlim(-6.5, 6.5) +
        #ylim(0, 100) +

        #Set title
        ggtitle(main) +

        #Tidy the text labels for a subset of genes
        geom_text(data=subset(toptable, FDR<LabellingCutoff & abs(logFC)>FCCutoff),
            aes(label=rownames(subset(toptable, FDR<LabellingCutoff & abs(logFC)>FCCutoff))),
            size=2.25,
            #segment.color="black", #This and the next parameter spread out the labels and join them to their points by a line
            #segment.size=0.01,
            check_overlap=TRUE,
            vjust=1.0) +

        #Add a vertical line for fold change cut-offs
        geom_vline(xintercept=c(-FCCutoff, FCCutoff), linetype="longdash", colour="black", size=0.4) +

        #Add a horizontal line for P-value cut-off
        geom_hline(yintercept=-log10(AdjustedCutoff), linetype="longdash", colour="black", size=0.4)

    return(plot)
}

Requires

• ggplot2

Execution

• EnhancedVolcanoDESeq2(topTable, NominalCutoff, AdjustedCutoff, LabellingCutoff, FCCutoff, main)
• EnhancedVolcanoEdgeR(topTable, NominalCutoff, AdjustedCutoff, LabellingCutoff, FCCutoff, main)

Example

• EnhancedVolcanoDESeq2(topTable=results, AdjustedCutoff=0.05, LabellingCutoff0.05, FCCutoff=2.0, main="DESeq2 results")
• EnhancedVolcanoEdgeR(topTable=results, AdjustedCutoff=0.05, LabellingCutoff0.05, FCCutoff=2.0, main="EdgeR results")

Parameters

• toptable, data-frame of test statistics. Requires at least the following
• gene names as rownames
• column named 'log2FoldChange' for DESeq2 or 'logFC' for EdgeR
• column named 'padj' for DESeq2 or 'FDR' for EdgeR
• NominalCutoff, nominal p-value cut-off for statistical significance (obsolete)
• AdjustedCutoff, adjusted p-value cut-off for statistical significance
• LabellingCutoff, adjusted p-value cut-off for statistical significance for labels
• FCCutoff, absolute log (base 2) fold change cut-off for statistical significance
• main, title

Oh, sure, you can add any number of lines with the following parameters:

EnhancedVolcano(
  ...
  hline = c(10e-12, 10e-36, 10e-60, 10e-84),
  hlineCol = c('grey0', 'grey25','grey50','grey75'),
  hlineType = 'longdash',
  hlineWidth = 0.8,
  ...)

For vertical lines, they are:

vline
vlineCol
vlineType
vlineWidth

You can add any number of lines.

Then, there are also the main cut-off lines:

cutoffLineType
cutoffLineCol
cutoffLineWidth

...and the standard ggplot2 engine lines:

gridlines.major = FALSE
gridlines.minor = FALSE

[source: https://github.com/kevinblighe/EnhancedVolcano#adjust-cut-off-lines-and-add-extra-threshold-lines]