基于倍数富集的R中的着色散点图

Question

I'm very new to R and have tried to search around for an answer to my question, but couldn't find quite what I was looking for (or I just couldn't figure out the right keywords to include!). I think this is a fairly common task in R though, I am just very new.

I have ax vs y scatterplot and I want to color those points for which there is at least a 2-fold enrichment, ie where x/y>=2 . Since my values are expressed as log2 values, the the transformed value needs to be x/y>=4.

I currently have the scatterplot plotted with

plot(log2(counts[,40], log2(counts[,41))

where counts is a .csv imported files and 40 & 41 are my columns of interested.

I've also created a column for fold change using

counts$fold<-counts[,41]/counts[,40]

I don't know how to incorporate these two pieces of information... Ultimately I want a graph that looks something like the example here: http://s17.postimg.org/s3k1w8r7j/error_messsage_1.png where those points that are at least two-fold enriched will colored in blue.

Any help would be greatly appreciated. Thanks!

Answer 1

Is this what you're looking for:

# Fake data
dat = data.frame(x=runif(100,0,50), y = rnorm(100, 10, 2))

plot(dat$x, dat$y, col=ifelse(dat$x/dat$y > 4, "blue", "red"), pch=16)

The ifelse statement creates a vector of "blue" and "red" (or whatever colors you want) based on the values of dat$x/dat$y and plot uses that to color the points.

This might be helpful if you've never worked with colors in R .

Another option is to use ggplot2 instead of base graphics. Here's an example:

library(ggplot2)
ggplot(dat, aes(x,y, colour=cut(x/y, breaks=c(-1000,4,1000), 
                                labels=c("<=4",">4")))) + 
  geom_point(size=5) + 
  labs(colour="x/y")