Overlaid XY plot with two different colors for control and target genes

Question

[Chirag Nepal]

Hi all,

I have expression measure of genes (two sets: target and contro genes) as measured by RNAseq, which is computed in tabular matrix.

head(A)
                                          V1    V2    V3    V4    V5    V6
1 chr20:38788661-38812050_ENSDART00000136771 1.912 1.912 1.912 4.770 0.703
2  chr4:13971999-13980660_ENSDART00000067040 0.502 0.502 0.502 1.242 0.011

     V7     V8     V9    V10   V11    V12    V13
1 0.137  6.534  4.689  7.086 2.646  4.376  0.684
2 0.007  0.684  1.125  2.819 2.392  1.406  0.364
head(B)
                                          V1    V2    V3    V4    V5    V6
1 chr19:24974067-24977991_ENSDART00000052421 0.005 0.005 0.005 0.025 0.139
2  chr8:26148102-26150871_ENSDART00000049793 2.312 2.312 2.312 6.153 1.109
3  chr8:47908733-47913950_ENSDART00000025620 2.446 2.446 2.446 9.660 5.411
     V7     V8     V9    V10   V11    V12    V13
1 0.807  0.010  0.232  5.963 0.022  0.149  3.162
2 0.291  4.556  3.214 16.486 2.158  5.599  0.939
3 7.745 11.614 13.150 51.680 8.557 18.356 36.378

PLOT:

par (mfrow=c(1,2))
plot (log2(A$V2/A$V5), log2(A$V8/A$V11), xlab="log2(FC)", ylab="log2(FC)", xlim=c(-5,5), ylim=c(-5,5), col="red")
abline(v=0, lty=2); abline (h=0, lty=2)
plot (log2(B$V2/B$V5), log2(B$V8/B$V11), xlab="log2(FC)", ylab="log2(FC)", col="blue", xlim=c(-5,5), ylim=c(-5,5))
abline(v=0, lty=2); abline (h=0, lty=2)

How could i plot both in the same plot?

cheers

Chirag

[Chirag Nepal]

Thank you very much guys !!

Answer 1

[Jason]

If I were you I would try using your first plot as is, but for the second plot instead of using the plot function, use points e.g.

plot (log2(A$V2/A$V5), log2(A$V8/A$V11), xlab="log2(FC)", ylab="log2(FC)", xlim=c(-5,5), ylim=c(-5,5), col="red")
points(log2(B$V2/B$V5), log2(B$V8/B$V11),  col="blue")
abline(v=0, lty=2); abline (h=0, lty=2)

You could also use par(new=TRUE) instead. i.e.

plot (log2(A$V2/A$V5), log2(A$V8/A$V11), xlab="log2(FC)", ylab="log2(FC)", xlim=c(-5,5), ylim=c(-5,5), col="red")
par(new =TRUE)
plot (log2(B$V2/B$V5), log2(B$V8/B$V11), xlab="", ylab="", col="blue", xlim=c(-5,5), ylim=c(-5,5))
abline(v=0, lty=2); abline (h=0, lty=2)

edit:

Also, if the A$V2 etc doesn't work you may want to use A[,2] instead.

Answer 2

[Devon Ryan]

cols=c(rep("red",2),rep("blue",3))
with(rbind(A,B), plot(log2(V2/V5), log2(V8/V11), xlab="log2(FC)", ylab="log2(FC)", xlim=c(-5,5), ylim=c(-5,5), col=cols))
abline(v=0, lty=2); abline (h=0, lty=2)

You could also just add the colors as a column, which would make life easier if using ggplot2.

Answer 3

[Ido Tamir]

a)

plot(c(log2(A$V2/A$V5),log2(B$V2/B$V5)), c(...), col=c(rep("red", nrow(A)),rep("blue", nrow(B)))

b)

with ggplot2 its much more elegant. You would have to create one data frame with a structure like:

gene name    x        y        type
gene1        3.2      1.2      control
....             
geneN        1.2      3.2      target

and then ggplot(df, aes(x=x,y=y, colour=type))+geom_point()