Difference between revisions of "2018 June Taeyoung Lab note"
From Crop Genomics Lab.
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library(UpSetR) | library(UpSetR) | ||
upset(Data,sets = c("Lus","Ptr","Rco","Jcu","Mes","Hbr"),order.by="freq",empty.intersections="on") | 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$Gene | ||
| + | pheatmap(log(Data[2:5]+1),color = colorRampPalette(c("white","firebrick3"))(50),cluster_cols = FALSE, cluster_rows = FALSE) | ||
Latest revision as of 04:33, 6 October 2018
UpSetR plot
library(UpSetR)
upset(Data,sets = c("Lus","Ptr","Rco","Jcu","Mes","Hbr"),order.by="freq",empty.intersections="on")
pheatmap
library(pheatmap)
Data<-read.table("PE_gene_list.txt.RPKM",header=T)
head(Data)
Gene B Y G I 1 Jatcu.01g001630 0.777053 0.900879 1.93941 4.831030 2 Jatcu.02g000639 3.246920 3.148340 23.04090 35.914500 3 Jatcu.02g000941 12.631700 13.201900 23.73470 14.621300 4 Jatcu.02g000968 7.888650 3.338680 4.60163 10.876700 5 Jatcu.02g001631 5.646930 7.952740 4.64940 5.600850 6 Jatcu.03g000784 3.271440 3.703690 1.34210 0.956547
rownames(Data)=Data$Gene
pheatmap(log(Data[2:5]+1),color = colorRampPalette(c("white","firebrick3"))(50),cluster_cols = FALSE, cluster_rows = FALSE)
