Question: How do I modify default ggplot2 axis?
0
gravatar for jaqx008
29 days ago by
jaqx00840
jaqx00840 wrote:

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 • 160 views
ADD COMMENTlink modified 29 days ago by rjactonspsfcf80 • written 29 days ago by jaqx00840
2
gravatar for rjactonspsfcf
29 days ago by
Southampton
rjactonspsfcf80 wrote:

just add limits

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

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

ADD COMMENTlink written 29 days ago by rjactonspsfcf80

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

ADD REPLYlink written 29 days ago by jaqx00840
2

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

ADD REPLYlink modified 29 days ago • written 29 days ago by Medhat8.0k

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

ADD REPLYlink written 29 days ago by jaqx00840
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