Question: Scatter plot by cummeRbund
gravatar for saj98
3.1 years ago by
saj98110 wrote:

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

> 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
rna-seq R • 1.1k views
ADD COMMENTlink modified 3.1 years ago by theobroma221.1k • written 3.1 years ago by saj98110

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

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

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by WouterDeCoster44k
gravatar for theobroma22
3.1 years ago by
theobroma221.1k wrote:

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.

ADD COMMENTlink written 3.1 years ago by theobroma221.1k
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