#!/usr/bin/Rscript
# Usage: Rscript long2wide.R . input prefixofoutput

args<-commandArgs(TRUE)
#################################################
# R包加載，這里展示跨用戶/跨版本調(diào)用R包
myPaths <- .libPaths()
new <- c("/home/xiaoshuai/R/x86_64-pc-linux-gnu-library/3.5","/home/xiaofang/R/x86_64-pc-linux-gnu-library/3.4")
myPaths <- c(myPaths, new)
.libPaths(myPaths)
library("tidyr", quietly = T,lib.loc="/home/xiaoshuai/R/x86_64-pc-linux-gnu-library/3.5")

#################################################
#工作目錄，傳入第一個參數(shù),即讀入與輸出數(shù)據(jù)所在的位置
setwd(args[1])
#setwd(".")

#################################################
#長數(shù)據(jù)的讀入，傳入第二個參數(shù)，即特定格式的輸入數(shù)據(jù)

data <- read.table(args[2],header=F)
#data <- read.table("aaa",header=FALSE)

data <- as.data.frame(data)
colnames(data) <- c("Count","Class","Group")

#################################
#長變寬
widedata1 <- spread(data,key = "Class",value = "Count")
widedata1[is.na(widedata1)]<-0
widedata2 <- spread(data,key = "Group",value = "Count")
widedata2[is.na(widedata2)]<-0

#################################
#寬數(shù)據(jù)輸出，傳入第三個參數(shù)，即輸出文件的前綴
output=as.character(args[3])
#output=as.character("bbb")
write.table(widedata1,paste(output,".v1.wide",sep=""),col.names =TRUE,row.names = FALSE,quote=F,sep = "\t") 
write.table(widedata2,paste(output,".v2.wide",sep=""),col.names =TRUE,row.names = FALSE,quote=F,sep = "\t") 

此模板以shell語言下經(jīng)常用到的長數(shù)據(jù)變寬數(shù)據(jù)為例
輸入數(shù)據(jù) aaa，第一列必須為計數(shù)，二三列不特殊要求，不含列命

cat aaa
23 gene1 grape
24 gene2 grape
67 gene3 rice
88 gene2 rice
13 gene3 grape

run:

Rscript long2wide.R . aaa bbb

得到兩個文件,以bbb為前綴

cat bbb.v1.wide
Group   gene1   gene2   gene3
grape   23      24      13
rice    0       88      67

cat bbb.v2.wide
Class   grape   rice
gene1   23      0
gene2   24      88
gene3   13      67