Question: Scatter plot by cummeRbund
0
gravatar for saj98
23 months ago by
saj98100
saj98100 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

>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
rna-seq R • 751 views
ADD COMMENTlink modified 23 months ago by theobroma221.1k • written 23 months ago by saj98100

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 23 months ago • written 23 months ago by WouterDeCoster39k
1
gravatar for theobroma22
23 months ago by
theobroma221.1k
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 23 months ago by theobroma221.1k
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