Scatter plot by cummeRbund

Question

[saj98]

Hello Everyone

I am using cummeRbund package to create scatter plot. I need help to guide me how to present the significant genes in different color. I tried the following codes, but it did not work, and I am attaching my figure. Does anybody have any idea how to change the color? Thanks for help

>library(cummeRbund)
>cuff<-readCufflinks()
> cuff
> s<-csScatterMatrix(genes(cuff))
> s
> m<-MAplot(genes(cuff),"q3","q6")
> m
>m <- fpkmMatrix(genes(cuff))
> cor(m[, 1], m[, 6])
> s<-csScatter(genes(cuff),"q3","q6",smooth=T)
> s
> s<-csScatter(genes(cuff),"q3","q6",smooth=T, showSignificant=TRUE, alpha=0.05, mapping=aes(size=5))
> s

[WouterDeCoster]

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This is not the first time that I have to tell you this. Please take this into account when asking questions.

Answer 1

[theobroma22]

From the manual, the scatter plot is not used to show groups of genes, so this functionality may not be doable from inside cummerbund. However you may be able to use ggplot2 and designate your genes using the group argument as an aesthetics.