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Draw a pca diagram of plink data in R

Hi, I want to plot P C 1 and P C 2 of plink .ei genvec data in R but there is a problem I can not use all the file samples in the chart. Thankful

r plink pca
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written by mohsen • mohsen

Hello mohsen!

This question in its current form does not look related to bioinformatics. Please add more detail on what this question is about and what you've tried.

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written by Ram Ram

How do you expect us to help you if you don't show any code or error?

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written by WouterDeCoster WouterDeCoster

Hi, I got the following error with this command code:

col <-c("breed1"="red" ,"breed2"="yellow" ,"breed3"="green" ,"breed4"="orange" ,"breed5"="brown" ,"breed6"="pink" ,"breed7"="maroon" ,"breed8"="cyan" ,"breed9"="firebreck1" ,"breed10"="blue" ,"breed11"="bisque" ,"breed12"="chartreuse4")
tab1 %>% mutate(group=substr(breeds,1,3))  %>% ggplot(.,aes(x=PC1,y=PC2))  +
+ geom_point (aes(colour=breeds))+scale_color_manual(values=col)

Error: Insufficient values in manual scale. 121 needed but only 12 provided.
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updated by Ram Ram • written by mohsen • mohsen

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