No subscript and hgnc symbols display in volcano plots

Question

[Nicky]

hi guys, I am making a volcano plot and so far have this: (I am new in R, just a couple of days of experience so excuse me if I made something silly).

setwd("Gene_R_coding")

padj<- RNAseq[RNAseq$padj<=0.01,]

FC<- subset(padj,abs(log2FoldChange)>=1)

write.csv(FC,file="CMP_FC.csv")

plot<- with(RNAseq,plot(RNAseq$log2FoldChange,-log10(RNAseq$padj),
                            main="VolcanoPlot",
                            xlab="Effect size: fold-change (Log[2])",
                            ylab="-Log[10] (adj.p-value)",
                            ylim=c(0,90), 
                            pch=20,                
                            abline(h=-log10(0.01),
                                   col="blue",
                                   lty="1343",
                                   lwd="2",
                                   abline(v=c(-2,2),
                                          col="blue",
                                          lty= "1343",
                                          lwd= "2",
                                          abline(v=c(0),
                                                 col="blue",
                                                 lty= "1343",


                                          )))))

            with(subset(RNAseq,padj<0.01),points(log2FoldChange,-log10(padj),pch=20,col="red"))
                  with(subset(RNAseq,padj<0.01 & abs(log2FoldChange)<2),points(log2FoldChange,-log10(padj),pch=20,col="lightgrey"))
                  with(subset(RNAseq,padj<0.01 & log2FoldChange>2),points(log2FoldChange,-log10(padj),pch=20,col="green3"))
                         with(subset(RNAseq,padj>0.01),points(log2FoldChange,-log10(padj),pch=20,col="lightgrey"))


                            hgnc_symbol <- abs(RNAseq$log2FoldChange) > 5 & RNAseq$padj<0.001
                                text(RNAseq$log2FoldChange[hgnc_symbol],
                                   -log10(RNAseq$padj)[hgnc_symbol],
                                               lab=rownames(RNAseq)[hgnc_symbol], cex=0.5)

for some reasons the volcano plot do not display the subscript even after brakets addition in log[2] and log[10] any idea why?

the other problem is that the volcano plot does not display the hgnc_symbol, it gave me numbers instead!

my data set has the following headers

    ensembl HGNC.ID NCBI.gene.ID    Predicted.HGNC.symbol   hgnc_symbol baseMean    log2FoldChange  lfcSE   stat    pvalue  padj

[cpad0112]

Nicky

Try this for subscript issues:

plot(1:10,xlab=expression('Effect size: fold-change (Log'[2]*')'), ylab=expression('-Log'[10]*'(adj.p-value)'))

For hgnc_symbol, looking at the df structure may help.

[Nicky]

Hi, thank you very much,

The subscript actually worked!

I haven't been lucky to get the gene name, what do you mean by "looking at the df structure"

thanks again

[cpad0112]

try printing this: rownames(RNAseq)[hgnc_symbol] and str(rownames(RNAseq)[hgnc_symbol])