How do I modify default ggplot2 axis?

Hello everyone I have an r script that I used sometime ago to make scattered plots. But The scattered plotes generated by the script adjusted according to the data i provided it. now I am trying to modify the R script to specific axis like x-axis min=-5, max=5. y-axis min=-5 max=5 see my script below thanks.

#!/usr/bin/env Rscript
library(ggplot2)
DE <- read.csv("Scored.txt", header = FALSE, sep = "\t")
DE[,2] <- log(DE[2], 2)
pdf("scatterplot.pdf")
ggplot(DE, aes(x = DE$V2, y = DE$V3, color = DE$V8, pch = DE$V7 > .05)) + geom_point(alpha = 1/2) + geom_rug(sides = "l") + theme_minimal() +
labs (x = "Log Mean Expression", y = "Log2 Fold Change", pch = "P-value > 0.5", color = "Category", size = 48)
dev.off()

How can I add the command to adjust the axis as specified above?

rna-seq deseq2 ggplot2 rscript

• 2,836 views • link

updated 7.8 years ago by rjactonspsfcf

• written 7.8 years ago by jaqx008

1 answer

just add limits

<plot object> + xlim(-5,5) + ylim(-5,5)

see: https://ggplot2.tidyverse.org/reference/lims.html

• 1 views • link

written 7.8 years ago by rjactonspsfcf

Where in the code could this fit in? thanks Ive tried adding the limits but not sure were it should be cos I keep getting error messages from terminal

• 1 views • link

written 7.8 years ago by jaqx008

let

p -> ggplot(DE, aes(x = DE$V2, y = DE$V3, color = DE$V8, pch = DE$V7 > .05)) + geom_point(alpha = 1/2) + geom_rug(sides = "l") + theme_minimal() +
labs (x = "Log Mean Expression", y = "Log2 Fold Change", pch = "P-value > 0.5", color = "Category", size = 48)

Then the code will be

p + xlim(-5,5) + ylim(-5,5)

Please refer to as suggested by rjactonspsfcf

https://ggplot2.tidyverse.org/reference/lims.html

• 1 views • link

written 7.8 years ago by Medhat

Thanks Guys. It works now but without the p. I appreciate it. :)

• 1 views • link

written 7.8 years ago by jaqx008