2018 June Taeyoung Lab note

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UpSetR plot

library(UpSetR)
upset(Data,sets = c("Lus","Ptr","Rco","Jcu","Mes","Hbr"),order.by="freq",empty.intersections="on")

pheatmap

library(pheatmap)
Data<-read.table("PE_gene_list.txt.RPKM",header=T)
head(Data)
            Gene         B         Y        G         I

1 Jatcu.01g001630 0.777053 0.900879 1.93941 4.831030 2 Jatcu.02g000639 3.246920 3.148340 23.04090 35.914500 3 Jatcu.02g000941 12.631700 13.201900 23.73470 14.621300 4 Jatcu.02g000968 7.888650 3.338680 4.60163 10.876700 5 Jatcu.02g001631 5.646930 7.952740 4.64940 5.600850 6 Jatcu.03g000784 3.271440 3.703690 1.34210 0.956547

rownames(Data)=Data$Gene
pheatmap(log(Data[2:5]+1),color = colorRampPalette(c("white","firebrick3"))(50),cluster_cols = FALSE, cluster_rows = FALSE)