No subscript and hgnc symbols display in volcano plots
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20 months ago
Nicky • 0

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],
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

RNA-Seq gene volcano plot • 483 views
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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.

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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

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