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Question: Deseq2 PCA plot customize
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gravatar for jarod_v6@libero.it
14 months ago by
Italy
jarod_v6@libero.it20 wrote:

How can choose the color use on   pca plot. I have many samples but I want to have a set of colors:

 

 

data<-DESeq2::plotPCA(rld,intgroup=c("condition"),returnData=TRUE)
p1<-qplot(PC1,PC2,color=condition,data=data,size=I(10))
ggsave("PCA_condition.png",p1)

 

plotPCA(rld,intgroup=c("condition","id"),ntop=2000,color=brewer.pal(4,"Dark2"))
Error in .local(object, ...) :
  unused argument (color = c("#1B9E77", "#D95F02", "#7570B3", "#E7298A"))
> plotPCA(rld,intgroup=c("condition","id"),ntop=2000,col=brewer.pal(4,"Dark2"))
Error in .local(object, ...) :
  unused argument (col = c("#1B9E77", "#D95F02", "#7570B3", "#E7298A"))


 

and how can I plot with the labels of the samples.

Thanks s much!

 

 

 

 

 

ADD COMMENTlink modified 14 months ago by Michael Love11k • written 14 months ago by jarod_v6@libero.it20
3
gravatar for Michael Love
14 months ago by
Michael Love11k
United States
Michael Love11k wrote:

The best way to customize the plot is to use plotPCA to return a small data.frame and then use ggplot2 to customize the graph.

If you look in the vignette, search for the sentence "It is also possible to customize the PCA plot using the ggplot function."

vignette("DESeq2")
ADD COMMENTlink written 14 months ago by Michael Love11k
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