K-Science.info

K-Science.info

Structure Population Genetics:

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Running Structure

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Determining the Number of Clusters (K) using Structure Harvester

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Generating Summary Bar Charts using R Studio

p<-ggplot(ff,aes(x=factor(V1),y=(100*Freq),fill=factor(Var1))) + 
    geom_bar(position = "fill", stat = "identity")+
    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust=1, size=15))+
    theme(axis.text.y = element_text(angle = 0, hjust = 1, vjust=1, size=20))+
    theme(legend.title = element_text(size=20, face = "bold"))+
    theme(plot.title = element_text(size = 44, face = "bold", hjust = 0.5))+
    scale_y_continuous(labels = percent)+
    ggtitle("Structure Hibiscus ISSR Clustering Chart, K=3")+
    theme(axis.title.y = element_text(size = 20, angle = 90))+
    theme(axis.title.x = element_text(size = 20, angle = 360))
p+labs(fill = "Cluster",x = "Samples", y = "Percent %")


  
    
p<-ggplot(ff,aes(x=factor(pltype),y=(100*Freq),fill=factor(Var1))) + 
    geom_bar(position = "fill", stat = "identity")+
    theme(axis.text.x = element_text(angle = 75, hjust = 1, vjust=1, size=15))+
    theme(axis.text.y = element_text(angle = 0, hjust = 1, vjust=1, size=20))+
    theme(legend.title = element_text(size=20, face = "bold"))+
    theme(plot.title = element_text(size = 44, face = "bold", hjust = 0.5))+
    ggtitle("Structure Hibiscus ISSR Clustering Chart, K=3")+
    theme(axis.title.y = element_text(size = 20, angle = 90))+
    theme(axis.title.x = element_text(size = 20, angle = 360))
p+labs(fill = "Cluster",x = "Samples", y = "Frequency")
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p<-ggplot(ff,aes(x=factor(SP_LOC),y=Freq,fill=factor(Var1))) + 
    geom_bar(position = "fill", stat = "identity")+
    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust=1, size=15))+
    theme(axis.text.y = element_text(angle = 0, hjust = 1, vjust=1, size=20))+
    theme(legend.title = element_text(size=20, face = "bold"))+
    theme(plot.title = element_text(size = 44, face = "bold", hjust = 0.5))+
    ggtitle("Amaranthus palmeri Clustering Chart, K=2")+
    theme(axis.title.y = element_text(size = 20, angle = 90))+
    theme(axis.title.x = element_text(size = 20, angle = 360))
p+labs(fill = "Cluster",x = "Samples", y = "Frequency")
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