R scatter plot visualization: how to color custom- multiple genes into scatter plot?

Question

[choijamtsm]

Hello everyone!

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

#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

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

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!

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!

Answer 1

[Kevin Blighe]

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)

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)