Hello everyone!

I tried to make a basic scatter plot with R using gene expression data.

```r
#import data: 

oldmice <- read.table("oldmice.txt", header = TRUE)
youngmice <- read.table("youngmice.txt", header = TRUE)
```
 
Imported data contains: format is the same for both  imported data but MGE has different values.

     gene	MGE
    Sox17	-6.74193774617653	
    Mrpl15	-0.212567471203473	
    Lypla1	-0.711251006455475	

and so on.. 

 Made basic volcano plot using: youngmice$MGE vs oldmice$MGE

```r
plot(oldmice$MGE, youngmice$MGE, main="old vs young mice!!",
     xlab="oldmice$MGE ", ylab="youngmice$MGE ", pch=19)
```

My question is how to color  "genes" which is in `multiple_gene_lists` into `oldmice$MGE`, `youngmice$MGE`? (which should label the only `multiple_gene_list` which are in `multiple_gene_lists` into `oldmice$MGE`, `youngmice$MGE`)

Here is my multiple_gene_list

```r
multiple_gene_list <- read.table("multiple_gene_list.txt", header = TRUE)
multiple_gene_list  <- as.vector(multiple_gene_list )
```

`multiple_gene_list` contains:

    gene
    Six6
    Arl2
    Tmem74B
    Rab9B
    Rasgef1B
    Ccne1
    Apln
    Spag7
    C17Orf59
    Krtap4-4

And my goal is to only label `multiple_gene_list` in `oldmice$MGE`, `youngmice$MGE`. I also tried the following code but failed!

```r
with(subset(ASC_oldmice_exprs, ASC_oldmice_exprs$gene %in%  multiple_gene_list$gene), points(ASC_youngmice_exprs$MGE, pch=20, col="red"))
```

Thank you!
Hey, here is a simple way to do it, and to also have a different shape for the genes of interest:

    oldmice <- data.frame(gene = c("BRCA1","BRCA2","BRCC3","TP53","ATM"),
      MGE = c(-6,-5,-8,-7,-6))
    youngmice <- data.frame(gene = c("BRCA1","BRCA2","BRCC3","TP53","ATM"),
      MGE = c(-6.5,-7,-4,-7,-8))
    multiple_gene_list  <- c("TP53","ATM")
    
1, Create a default colour vector:
----
    mycol <- rep("grey50", length(youngmice$gene))
    mycol
    [1] "grey50" "grey50" "grey50" "grey50" "grey50"

2, Set a colour for the genes of interest:
----
    mycol[which(youngmice$gene %in% multiple_gene_list)] <- "firebrick1"
    mycol
    [1] "grey50"     "grey50"     "grey50"     "firebrick1" "firebrick1"

3, Same as 1 & 2 but for shape (pch):
----
    mypch <- rep(19, length(youngmice$gene))
    mypch[which(youngmice$gene %in% multiple_gene_list)] <- 18
    mypch
    [1] 19 19 19 18 18

4, Plot data:
----
    plot(oldmice$MGE, youngmice$MGE, main = "old vs young mice!!",
      xlab = "oldmice$MGE ", ylab = "youngmice$MGE ", pch = mypch, col = mycol, cex = 5.0,
      xlim = c(-10, -2), ylim = c(-10, -2))

    text(
      subset(oldmice, gene %in% multiple_gene_list)$MGE,
      subset(youngmice, gene %in% multiple_gene_list)$MGE - 0.45,
      lab = subset(youngmice, gene %in% multiple_gene_list)$gene,
      cex = 1.0)


<a href="https://ibb.co/BfDVKVK"><img src="https://i.ibb.co/qDGMFMF/f.png" alt="f" border="0"></a>

You can also set the labels this way:

    mylab <- as.character(youngmice$gene)
    mylab[-which(youngmice$gene %in% multiple_gene_list)] <- ""
    mylab
    [1] ""     ""     ""     "TP53" "ATM"

    plot(oldmice$MGE, youngmice$MGE, main = "old vs young mice!!",
      xlab = "oldmice$MGE ", ylab = "youngmice$MGE ", pch = mypch, col = mycol, cex = 5.0,
      xlim = c(-10, -2), ylim = c(-10, -2))

    text(oldmice$MGE, youngmice$MGE - 0.45,
      lab = mylab,
      cex = 1.0)

<a href="https://imgbb.com/"><img src="https://i.ibb.co/7Nxq8yr/h.png" alt="h" border="0"></a>
