I have a set of genes from an RNA-seq dataset generated from Wild type and mutant samples. As expected there are a number of genes that significantly differ in gene expression as called by Cufflinks/cuffdiff.
I am trying to create a scatterplot where the genes that significantly change in expression are colored differently than the genes that do not (ex.: Up = red, down = blue, NS = black).
However I can only seem to figure out how to create individual plots in a single color (like only showing the points that are significantly up-regulated in red, but no other points).
I would like to make a single graph with all of the genes plotted, and with the significantly changing genes in specific colors (perhaps even point sizes!). I'm fairly new to using R so any help would really be appreciated.
I have lists of these genes and have generated gene lists using:
>myDOWNGenesIds <- read.table("down>2.txt")
>myDOWNGenes <- getGenes(cuff,myDOWNGenesIds[ ,1])
And I can generate individual scatterplots using:
>s <- csScatter(genes(cuff), "Wild_Type", "Mutant")
>sDown <- csScatter(myDOWNGenes, "Wild_Type", "Mutant")
I can also change aspects of these individual graphs:
>sDown + geom_point(size=3, color="red")