Dear Biostars, Hi

I have a **volcano** plot (obtained from edgeR). I also have **some selected annotated genes** that I like to highlight them by **showing** only their name on that plot. 

I have used the [valuable script/code][1] from Biostars (thank you @WouterDeCoster and @venu and others).

As most of the lines of the first column in my *counts.matrix* is empty (I have only about 15 names), I received some errors. For example, in the "Head" example below, I have only **PAC1** and **Gh** as Gene name and the other lines have "**space**" instead of any Gene name!

would you please check my script and my counts.matrix example and help me in this regard? Thanks

NOTE:

1- Head of my counts.matrix file:

    Gene	external_gene_name	logFC	logCPM	P.Value	FDR
    PAC1	TRINITY_c0_g2_i4	-13.8732718193368	4.61855606743036	3.03811154383156e-30	1.87897780840196e-24
     	TRINITY_c5_g3_i4	13.2697070220115	4.01618042373378	1.21936893870205e-27	3.7707094407506e-22
    GH	TRINITY_c9_g2_i2	11.2269211011449	3.82178000481344	3.20153046019011e-26	6.60015780727773e-21
     	TRINITY_c0_g1_i1	12.855465908739	3.60335598332695	2.98018910927419e-24	4.60788644555924e-19
     	TRINITY_c0_g1_i1	-11.8727923903381	2.62735890209779	1.81499535997098e-20	2.24503673057178e-15
     	TRINITY_c6_g1_i6	10.3243429332541	2.89490936855587	2.16106621247948e-19	2.22758743227662e-14
     	TRINITY_g3_i2	-12.0236467730875	2.77706530918009	2.63166646685828e-19	2.32514875441625e-14
     	TRINITY_c3_g2_i6	-11.2400737828536	2.00142608642608	1.40238473598696e-18	1.0841643566014e-13 	
        TRINITY_c1_g1_i1	-9.45052158373113	2.158090406858	1.66695714263313e-18	1.14551257449686e-13


2- my code:


        # Load packages
        library(dplyr)
        library(ggplot2)
        library(ggrepel)
        
        # Read data 
        data <- read.table("trans.counts.matrix.J_vs_M.edgeR.DE_results", header=TRUE)
        
        data$threshold = as.factor(data$FDR < 0.001)
        
    
        data = mutate(data, sig=ifelse(data$FDR<0.001, "FDR<0.001", "Not Sig"))
        
        p = ggplot(data, aes(logFC, -log10(P.Value))) +
          geom_point(aes(col=sig)) +
          scale_color_manual(values=c("red", "black"))
        
        p
      p+geom_text_repel(data=filter(data, FDR<0.001), aes(label=Gene))
        
        




  [1]: https://www.biostars.org/p/203876/
Change this line of code

    data <- read.table("trans.counts.matrix.J_vs_M.edgeR.DE_results", header=TRUE)

to

    data <- read.delim("trans.counts.matrix.J_vs_M.edgeR.DE_results", header=TRUE, na.strings=c("","NA"))

This adds `<NA>` to empty cells which will be ignored in the plot and only gene names will be added.

