Hi, Try this:
directory<- "/home/arunksa111/dados"
GetFileList <- function(directory,number){
setwd(directory)
filelist1<-dir()[file.info(dir())$isdir]
direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
direct<-lapply(direct,function(x) paste(directory,"/",x,sep=""))
lista<-unlist(direct)
output<- list(filelist1,lista)
return(output)
}
file.list.names<-GetFileList(directory,23)[[1]]
lista<-GetFileList(directory,23)[[2]]
FacGroup<-c(0,1,0,2,2,0,3)
ReadDir<-function(FacGroup){
list.new<-lista[FacGroup!=0]
read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep = "\t"))
names(read.list)<-file.list.names[FacGroup!=0]
return (read.list)
}
ListFacGroup<-ReadDir(FacGroup)
z.boxplotgroup<- function(lst){
lst1<- lapply(lst,function(x) x[x$FDR<0.01,])
library(plyr)
new.list<-lapply(split(lst1,gsub("\\d+","",names(lst1))),function(x)
join_all(lapply(x,function(x) x),type="full"))
par(mfrow=c(2,2))
b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
}
z.boxplotgroup(ListFacGroup)
z.boxplot<- function(lst){
new.list<- lapply(lst,function(x) x[x$FDR<0.01,])
#print(new.list)
par(mfrow=c(2,2))
b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
}
z.boxplot(ListFacGroup)
pdf("Veraboxplot.pdf")
z.boxplot(ListFacGroup)
z.boxplotgroup(ListFacGroup)
Joining by: Seq, Mod, z, score, FDR, Count, E, C, pos, spec, Pro
dev.off()
A.K.
________________________________
From: Vera Costa <veracosta...@gmail.com>
To: arun <smartpink...@yahoo.com>
Sent: Thursday, March 21, 2013 11:24 AM
Subject: Re: new question
Hi.
Thank you your help and sorry only answer now.
Ok, the boxplots is ok. But I need too by group... on par(mfrow(c(2,2))), I can
have par(mfrow(c(3,2)), for example (or more) and have a boxplot for the group.
You can help me to group them?
About the other function I need to do other things, but now I need to think
what to do...
Thank you
2013/3/18 arun <smartpink...@yahoo.com>
>
>
> z.boxplot<- function(lst){
> new.list<- lapply(lst,function(x) x[x$FDR<0.01,])
>print(new.list)
> par(mfrow=c(2,2))
>b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
>boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>
>}
> z.boxplot(ListFacGroup) #prints new.list
>
>If you want to turn off that:
>
> z.boxplot<- function(lst){
> new.list<- lapply(lst,function(x) x[x$FDR<0.01,])
>#print(new.list)
> par(mfrow=c(2,2))
>b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
>boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>
>
>}
> z.boxplot(ListFacGroup)
>A.K.
>
>
>
>
>
>________________________________
>From: Vera Costa <veracosta...@gmail.com>
>To: arun <smartpink...@yahoo.com>
>Sent: Monday, March 18, 2013 1:59 PM
>Subject: Re: new question
>
>
>
>For example, if I run you code without "pdf...." and "dev.off" I have what I
>want
>
>directory<- "C:/Users/Vera Costa/Desktop/dados.lixo"
> #modified the function
>GetFileList <- function(directory,number){
> setwd(directory)
> filelist1<-dir()
>
> lista<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
>full.names = TRUE, recursive = TRUE)
> output<- list(filelist1,lista)
> return(output)
> }
>file.list.names<-GetFileList(directory,23)[[1]]
>lista<-GetFileList(directory,23)[[2]]
>FacGroup<-c(0,1,0,2,2,0,3)
>ReadDir<-function(FacGroup){
> list.new<-lista[FacGroup!=0]
> read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
>"\t"))
> names(read.list)<-file.list.names[FacGroup!=0]
> return (read.list)
> }
>ListFacGroup<-ReadDir(FacGroup)
>ListFacGroup
> z.boxplot<- function(lst){
> new.list<- lapply(lst,function(x) x[x$FDR<0.01,])
> print(new.list)
> #pdf("VeraBP.pdf")
> par(mfrow=c(2,2))
> lapply(names(new.list),function(x) lapply(new.list[x],function(y)
>boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
> #dev.off()
> }
> z.boxplot(ListFacGroup)
>
>
>
>
>
>But I have the results too (I don't need it)
>
>
>[[1]]
>[[1]]$a2
>[[1]]$a2$stats
> [,1] [,2]
>[1,] 0.0000000000 0.0000000000
>[2,] 0.0000000000 0.0000000000
>[3,] 0.0001355197 0.0002175095
>[4,] 0.0010588777 0.0004350190
>[5,] 0.0016571381 0.0004350190
>[[1]]$a2$n
>[1] 8 2
>[[1]]$a2$conf
> [,1] [,2]
>[1,] -0.0004559846 -0.0002685062
>[2,] 0.0007270240 0.0007035253
>[[1]]$a2$out
>[1] 0.00494012
>[[1]]$a2$group
>[1] 1
>[[1]]$a2$names
>[1] "2" "3"
>
>[[2]]
>[[2]]$c2
>[[2]]$c2$stats
> [,1] [,2]
>[1,] 0.0000000000 0.0000000000
>[2,] 0.0000000000 0.0000000000
>[3,] 0.0001355197 0.0002175095
>[4,] 0.0010588777 0.0004350190
>[5,] 0.0016571381 0.0004350190
>[[2]]$c2$n
>[1] 8 2
>[[2]]$c2$conf
> [,1] [,2]
>[1,] -0.0004559846 -0.0002685062
>[2,] 0.0007270240 0.0007035253
>[[2]]$c2$out
>[1] 0.00494012
>[[2]]$c2$group
>[1] 1
>[[2]]$c2$names
>[1] "2" "3"
>
>[[3]]
>[[3]]$c3
>[[3]]$c3$stats
> [,1] [,2]
>[1,] 0.000000000 0.0000000000
>[2,] 0.000000000 0.0000000000
>[3,] 0.000000000 0.0000000000
>[4,] 0.002226409 0.0002086594
>[5,] 0.002226409 0.0004173187
>[[3]]$c3$n
>[1] 6 4
>[[3]]$c3$conf
> [,1] [,2]
>[1,] -0.001436105 -0.0001648409
>[2,] 0.001436105 0.0001648409
>[[3]]$c3$out
>[1] 0.00560348
>[[3]]$c3$group
>[1] 1
>[[3]]$c3$names
>[1] "2" "3"
>
>[[4]]
>[[4]]$t2
>[[4]]$t2$stats
> [,1] [,2] [,3]
>[1,] 0 0.0000000000 0
>[2,] 0 0.0000000000 0
>[3,] 0 0.0002908668 0
>[4,] 0 0.0025929827 0
>[5,] 0 0.0052577771 0
>[[4]]$t2$n
>[1] 1 10 5
>[[4]]$t2$conf
> [,1] [,2] [,3]
>[1,] 0 -0.001004691 0
>[2,] 0 0.001586424 0
>[[4]]$t2$out
>[1] 0.0092051934 0.0007174888
>[[4]]$t2$group
>[1] 2 3
>[[4]]$t2$names
>[1] "1" "2" "3"
>
Veraboxplot.pdf
Description: Adobe PDF document
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