No subscript and hgnc symbols display in volcano plots
0
0
Entering edit mode
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$log2FoldChange[hgnc_symbol],
                                   -log10(RNAseq$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
RNA-Seq gene volcano plot • 483 views
ADD COMMENT
0
Entering edit mode

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.

Rplot

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1219 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6