prepare_data_count.Rmd

Preprare Flaveria csv files
========================================================


```{r pringlei}
setwd("~/hydrogen/flaveria/Fp/Fp_2")
count <- read.csv("Fp_express.eff_count", sep="\t", head=T)
key <- read.csv('key_agi.txt',sep='\t', head=F)

setwd('~/hydrogen/flaveria/robin')
anno <- read.csv('robin_11.txt', sep="\t", head=F)
names(anno) <- c("species", "contig", "annotation")
anno$species <- gsub(anno$species, pattern="_200", replacement="")

library(plyr)
library(reshape2)
anno <- anno[which(anno$species=="Fp"),]

f_2 <- merge(count, anno, by.x="contig", by.y="contig")
f_2 <- f_2[,-c(2, 21,22)]
f_count <- ddply(f_2, .(annotation), numcolwise(sum))        # sum columns, grouping by annotation

setwd("~/hydrogen/flaveria")
write.table(f_count, file="fp.by_agi.count.csv", sep=",", row.names=FALSE)

```


```{r robusta}
setwd("~/hydrogen/flaveria/Fr/Fr_2")
count <- read.csv("Fr_express.eff_count", sep="\t", head=T)

setwd('~/hydrogen/flaveria/robin')
anno <- read.csv('robin_11.txt', sep="\t", head=F)
names(anno) <- c("species", "contig", "annotation")
anno$species <- gsub(anno$species, pattern="_200", replacement="")

library(plyr)
library(reshape2)
anno <- anno[which(anno$species=="Fr"),]

f_2 <- merge(count, anno, by.x="contig", by.y="contig")
f_2 <- f_2[,-c(2, 21,22)]
f_count <- ddply(f_2, .(annotation), numcolwise(sum))        # sum columns, grouping by annotation

setwd("~/hydrogen/flaveria")
write.table(f_count, file="fr.by_agi.count.csv", sep=",", row.names=FALSE)

```


```{r trinervia}
setwd("~/hydrogen/flaveria/Ft/Ft_2")
count <- read.csv("Ft_express.eff_count", sep="\t", head=T)

setwd('~/hydrogen/flaveria/robin')
anno <- read.csv('robin_11.txt', sep="\t", head=F)
names(anno) <- c("species", "contig", "annotation")
anno$species <- gsub(anno$species, pattern="_200", replacement="")

library(plyr)
library(reshape2)
anno <- anno[which(anno$species=="Ft"),]

f_2 <- merge(count, anno, by.x="contig", by.y="contig")
f_2 <- f_2[,-c(2, 21,22)]
f_count <- ddply(f_2, .(annotation), numcolwise(sum))        # sum columns, grouping by annotation

setwd("~/hydrogen/flaveria")
write.table(f_count, file="ft.by_agi.count.csv", sep=",", row.names=FALSE)

```


```{r bidentis}
setwd("~/hydrogen/flaveria/Fb/Fb_k")
count <- read.csv("Fb_express.eff_count", sep="\t", head=T)

setwd('~/hydrogen/flaveria/robin')
anno <- read.csv('robin_11.txt', sep="\t", head=F)
names(anno) <- c("species", "contig", "annotation")
anno$species <- gsub(anno$species, pattern="_200", replacement="")

library(plyr)
library(reshape2)
anno <- anno[which(anno$species=="Fb"),]

f_2 <- merge(count, anno, by.x="contig", by.y="contig")
f_2 <- f_2[,-c(2, 21,22)]
f_count <- ddply(f_2, .(annotation), numcolwise(sum))        # sum columns, grouping by annotation

setwd("~/hydrogen/flaveria")
write.table(f_count, file="fb.by_agi.count.csv", sep=",", row.names=FALSE)

```