y-axis on Volcano plot
1
0
Entering edit mode
3.4 years ago
jtehmsen ▴ 20

Hello,

I'm trying to generate a series of Volcano plots and would like the y-axes to be identical, but I keep getting the following message:

Error in UseMethod("limits") : 
  no applicable method for 'limits' applied to an object of class "NULL"

I am using the following code:

g <- ggplot(data=Complete_geneList_voom_limma, aes(x=logFC_KO.3.CTL_vs_WT.3.CTL, y=-log10(FDR_pVal_KO.3.CTL_vs_WT.3.CTL), colour=threshold)) + geom_point(alpha=0.4, size=1.75) + xlim(c(-6,6)) + ylim(c(0,15) + theme_bw() + theme(legend.position = "none") + scale_colour_manual(values=c("firebrick","navy")) + geom_vline(xintercept=1.5, linetype="dashed") + geom_vline(xintercept=-1.5, linetype="dashed") + geom_hline(yintercept=1.3, linetype="dashed")

Can anyone please help? Thank you.

RNA-Seq • 2.3k views
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1
Entering edit mode
3.4 years ago

Your ylim parenthesis needs to be closed after the vector.

You have

 ylim(
    c(0, 15) + theme_bw( ...

Try:

 ylim(
    c(0, 15)) + theme_bw( ...
ADD COMMENT
1
Entering edit mode

Thanks so much - sorry I missed that! I didn't relate the error message to a coding error. Thank you very much for your help.

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