Script_R_2020/globalmatrix_creation.R
In martinEcarnot/signe: Useful functions to handle spectra
## COMPRESSION DES SPECTRES EN UNE MATRICE ##
# nettoyage des variables de l'espace de travail
rm(list = ls())
source('C:/Users/avitvale/Documents/Script_R/SIGNE_load.R') ##### N'arrive pas à trouver le chemin "normal (dans signeG), comprends pas pourquoi
source('C:/Users/avitvale/Documents/Script_R/adj_asd.R')
source('C:/Users/avitvale/Documents/Script_R/asd_read.R')
# #création de la matrice qui rassemble tous les dossiers:
globalmatrix=matrix(ncol=2072)
setwd("C:/Users/avitvale/Documents/SIGNE")
for (a in 2017:2019){
setwd("C:/Users/avitvale/Documents/SIGNE") #Mettre ici le chemin d'accès au dossier contenant les spectres
setwd(as.character(a)) #On balaie les trois dossiers année
for (n in 1:length(dir())){
if ((dir()[n])=="Aude" | (dir()[n])=="Beaujolais" | (dir()[n])=="GDRautre" |(dir()[n])=="GDR96"){
lieu=substr(dir()[n],1,1) #On attribue au spectre un identifiant lieu selon sa parcelle d'origine : A, B, G ou g
if ((dir()[n])=="GDRautre"){
lieu='g'
}
setwd(as.character(dir()[n])) #On entre dans le sous-dossier.
for (m in 1:length(dir())){
if(substr(dir()[m],9,9)=="P"){ #on ne s'intéresse qu'au mesures effectuées en suivant la modalité P
em=paste(dir()[m], sep="")
w=SIGNE_load(em)
rownames(w)=paste(dir()[m],rownames(w),lieu) #On ajoute l'identifiant lieu au nom de chaque spectre
globalmatrix=rbind(globalmatrix, w)
}
}
setwd("../")
}
}
}
globalmatrix=globalmatrix[complete.cases(globalmatrix),]
#str(globalmatrix)
#Filtrage des noms non standardisés
iout=which(nchar(rownames(globalmatrix))>18)
# rownames(globalmatrix[iout,])
# unique(rownames(globalmatrix[which(substr(rownames(globalmatrix),1,8)=="20170612"),]))
globalmatrix <- globalmatrix[-iout,]
## Filtrage des spectres aberrants #Tous les spectres aberrants sont-ils filtrés par ce moyen ?
globalmatrix=globalmatrix[globalmatrix[,500]>0.6,] #Actuellement, 33 spectres jugés aberrants filtrés ici. (Dont 5 qui ne font pas partie de nos 10 clones étudiés..?)
globalmatrix=globalmatrix[globalmatrix[,1]<0.2,]
globalmatrix=globalmatrix[globalmatrix[,2000]<0.25,]
## Ajustement des sauts de detecteur (Montpellier: sauts ?? 1000 (651 eme l.o.) et 1800 (1451))
########globalmatrix=adj_asd(globalmatrix,c(602,1402))
## Reduction des variables (extremites bruitees)
globalmatrix=globalmatrix[,seq(51,ncol(globalmatrix)-30,1)]
# ###Ajout du cepage au nom de la ligne. Retire aussi les cépages/clones qui ne sont pas les 3/10 notres.
# ##Filtre en fonction du cepage
# titre=rownames(globalmatrix)
#
# ya=(substr(titre,11,13))== "015"
# yb=(substr(titre,11,13))== "169"
# yc=(substr(titre,11,13))== "685"
#
# yd=(substr(titre,11,13))== "222"
# ye=(substr(titre,11,13))== "509"
# yf=(substr(titre,11,13))== "787"
#
# yg=(substr(titre,11,13))== "471"
# yh=(substr(titre,11,13))== "525"
# yi=(substr(titre,11,13))== "747"
# yj=(substr(titre,11,13))== "877"
#
# ##Separation en 3 matrices
# spa=globalmatrix[ya,]
# spb=globalmatrix[yb,]
# spc=globalmatrix[yc,]
# spd=globalmatrix[yd,]
# spe=globalmatrix[ye,]
# spf=globalmatrix[yf,]
# spg=globalmatrix[yg,]
# sph=globalmatrix[yh,]
# spi=globalmatrix[yi,]
# spj=globalmatrix[yj,]
#
# ##Rajoute le nom du cepage au nom de la ligne à la place de P/T/N
# substr(rownames(spa),9,9)="C"
# substr(rownames(spb),9,9)="C"
# substr(rownames(spc),9,9)="C"
#
# substr(rownames(spd),9,9)="G"
# substr(rownames(spe),9,9)="G"
# substr(rownames(spf),9,9)="G"
#
# substr(rownames(spg),9,9)="S"
# substr(rownames(sph),9,9)="S"
# substr(rownames(spi),9,9)="S"
# substr(rownames(spj),9,9)="S"
#
# ##Recombine les 3 matrices pour reformer sp
# globalmatrix=rbind(spa,spb,spc,spd,spe,spf,spg,sph,spi,spj)
#Cette méthode est équivalente à ce qui précède, simplement les spectres dans la globalmatrix ne sont pas dans le même ordre.
for (i in 1:length(globalmatrix[,1])){
if (substr(rownames(globalmatrix)[i],11,13)=="015" | substr(rownames(globalmatrix)[i],11,13)=="169" | substr(rownames(globalmatrix)[i],11,13)=="685"){
substr(rownames(globalmatrix)[i],9,9)="C"
}
else if (substr(rownames(globalmatrix)[i],11,13)=="222" | substr(rownames(globalmatrix)[i],11,13)=="509" | substr(rownames(globalmatrix)[i],11,13)=="787"){
substr(rownames(globalmatrix)[i],9,9)="G"
}
else if (substr(rownames(globalmatrix)[i],11,13)=="471" | substr(rownames(globalmatrix)[i],11,13)=="525" | substr(rownames(globalmatrix)[i],11,13)=="747" | substr(rownames(globalmatrix)[i],11,13)=="877"){
substr(rownames(globalmatrix)[i],9,9)="S"
}
else {
substr(rownames(globalmatrix)[i],9,9)="A"
}
}
iout=which(substr(rownames(globalmatrix),9,9)=="A")
globalmatrix <- globalmatrix[-iout,]
str(globalmatrix)
a=matrix(ncol=1992)
b=matrix(ncol=1992)
c=matrix(ncol=1992)
d=matrix(ncol=1992)
e=matrix(ncol=1992)
f=matrix(ncol=1992)
g=matrix(ncol=1992)
h=matrix(ncol=1992)
i=matrix(ncol=1992)
j=matrix(ncol=1992)
k=matrix(ncol=1992)
l=matrix(ncol=1992)
m=matrix(ncol=1992)
n=matrix(ncol=1992)
o=matrix(ncol=1992)
p=matrix(ncol=1992)
q=matrix(ncol=1992)
r=matrix(ncol=1992)
colnames(a)=449:2440
colnames(b)=449:2440
colnames(c)=449:2440
colnames(d)=449:2440
colnames(e)=449:2440
colnames(f)=449:2440
colnames(g)=449:2440
colnames(h)=449:2440
colnames(i)=449:2440
colnames(j)=449:2440
colnames(k)=449:2440
colnames(l)=449:2440
colnames(m)=449:2440
colnames(n)=449:2440
colnames(o)=449:2440
colnames(p)=449:2440
colnames(q)=449:2440
colnames(r)=449:2440
# interm=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13)[1])),])
# if (length(interm[,1])==18){
# a=rbind(a,interm[1,])
# rownames(a)[length(a[,1])]=paste(substr(rownames(interm)[length(a[,1])],1,13),"-00 ", substr(rownames(interm)[length(a[,1])],18,18),1, sep="")
# # b=rbind(b,interm[2,])
# # c=rbind(c,interm[3,])
# # d=rbind(d,interm[4,])
# # e=rbind(e,interm[5,])
# # f=rbind(f,interm[6,])
# # g=rbind(g,interm[7,])
# # h=rbind(h,interm[8,])
# # i=rbind(i,interm[9,])
# # j=rbind(j,interm[10,])
# # k=rbind(k,interm[11,])
# # l=rbind(l,interm[12,])
# # m=rbind(m,interm[13,])
# # n=rbind(n,interm[14,])
# # o=rbind(o,interm[15,])
# # p=rbind(p,interm[16,])
# # q=rbind(q,interm[17,])
# # r=rbind(r,interm[18,])
# }
for (z in 1:length(unique(substr(rownames(globalmatrix),1,13)))) {
interm=globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13))[z]),]
# truc1=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13))[1]),])
# truc2=globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13))[1]),]
if (length(interm[,1])==18){
a=rbind(a,interm[1,])
K=as.character(paste(substr(rownames(interm)[1],1,13),"-01 ", substr(rownames(interm)[1],18,18), sep=""))
rownames(a)[length(a[,1])]=K
b=rbind(b,interm[2,])
K=as.character(paste(substr(rownames(interm)[2],1,13),"-01 ", substr(rownames(interm)[2],18,18), sep=""))
rownames(b)[length(b[,1])]=K
c=rbind(c,interm[3,])
K=as.character(paste(substr(rownames(interm)[3],1,13),"-01 ", substr(rownames(interm)[3],18,18), sep=""))
rownames(c)[length(c[,1])]=K
d=rbind(d,interm[4,])
K=as.character(paste(substr(rownames(interm)[4],1,13),"-01 ", substr(rownames(interm)[4],18,18), sep=""))
rownames(d)[length(d[,1])]=K
e=rbind(e,interm[5,])
K=as.character(paste(substr(rownames(interm)[5],1,13),"-01 ", substr(rownames(interm)[5],18,18), sep=""))
rownames(e)[length(e[,1])]=K
f=rbind(f,interm[6,])
K=as.character(paste(substr(rownames(interm)[6],1,13),"-01 ", substr(rownames(interm)[6],18,18), sep=""))
rownames(f)[length(f[,1])]=K
g=rbind(g,interm[7,])
K=as.character(paste(substr(rownames(interm)[7],1,13),"-07 ", substr(rownames(interm)[7],18,18), sep=""))
rownames(g)[length(g[,1])]=K
h=rbind(h,interm[8,])
K=as.character(paste(substr(rownames(interm)[8],1,13),"-07 ", substr(rownames(interm)[8],18,18), sep=""))
rownames(h)[length(h[,1])]=K
i=rbind(i,interm[9,])
K=as.character(paste(substr(rownames(interm)[9],1,13),"-07 ", substr(rownames(interm)[9],18,18), sep=""))
rownames(i)[length(i[,1])]=K
j=rbind(j,interm[10,])
K=as.character(paste(substr(rownames(interm)[10],1,13),"-07 ", substr(rownames(interm)[10],18,18), sep=""))
rownames(j)[length(j[,1])]=K
k=rbind(k,interm[11,])
K=as.character(paste(substr(rownames(interm)[11],1,13),"-07 ", substr(rownames(interm)[11],18,18), sep=""))
rownames(k)[length(k[,1])]=K
l=rbind(l,interm[12,])
K=as.character(paste(substr(rownames(interm)[12],1,13),"-07 ", substr(rownames(interm)[12],18,18), sep=""))
rownames(l)[length(l[,1])]=K
m=rbind(m,interm[13,])
K=as.character(paste(substr(rownames(interm)[13],1,13),"-13 ", substr(rownames(interm)[13],18,18), sep=""))
rownames(m)[length(m[,1])]=K
n=rbind(n,interm[14,])
K=as.character(paste(substr(rownames(interm)[14],1,13),"-13 ", substr(rownames(interm)[14],18,18), sep=""))
rownames(n)[length(n[,1])]=K
o=rbind(o,interm[15,])
K=as.character(paste(substr(rownames(interm)[15],1,13),"-13 ", substr(rownames(interm)[15],18,18), sep=""))
rownames(o)[length(o[,1])]=K
p=rbind(p,interm[16,])
K=as.character(paste(substr(rownames(interm)[16],1,13),"-13 ", substr(rownames(interm)[16],18,18), sep=""))
rownames(p)[length(p[,1])]=K
q=rbind(q,interm[17,])
K=as.character(paste(substr(rownames(interm)[17],1,13),"-13 ", substr(rownames(interm)[17],18,18), sep=""))
rownames(q)[length(q[,1])]=K
r=rbind(r,interm[18,])
K=as.character(paste(substr(rownames(interm)[18],1,13),"-13 ", substr(rownames(interm)[18],18,18), sep=""))
rownames(r)[length(r[,1])]=K
}
}
colnames(b)=(max(as.numeric(colnames(a)))+1):((max(as.numeric(colnames(a)))+1)+length(b[1,])-1)
colnames(c)=(max(as.numeric(colnames(b)))+1):((max(as.numeric(colnames(b)))+1)+length(c[1,])-1)
colnames(d)=(max(as.numeric(colnames(c)))+1):((max(as.numeric(colnames(c)))+1)+length(d[1,])-1)
colnames(e)=(max(as.numeric(colnames(d)))+1):((max(as.numeric(colnames(d)))+1)+length(e[1,])-1)
colnames(f)=(max(as.numeric(colnames(e)))+1):((max(as.numeric(colnames(e)))+1)+length(f[1,])-1)
#colnames(g)=(max(as.numeric(colnames(f)))+1):((max(as.numeric(colnames(f)))+1)+length(g[1,])-1)
colnames(h)=(max(as.numeric(colnames(g)))+1):((max(as.numeric(colnames(g)))+1)+length(h[1,])-1)
colnames(i)=(max(as.numeric(colnames(h)))+1):((max(as.numeric(colnames(h)))+1)+length(i[1,])-1)
colnames(j)=(max(as.numeric(colnames(i)))+1):((max(as.numeric(colnames(i)))+1)+length(j[1,])-1)
colnames(k)=(max(as.numeric(colnames(j)))+1):((max(as.numeric(colnames(j)))+1)+length(k[1,])-1)
colnames(l)=(max(as.numeric(colnames(k)))+1):((max(as.numeric(colnames(k)))+1)+length(l[1,])-1)
#colnames(m)=(max(as.numeric(colnames(l)))+1):((max(as.numeric(colnames(l)))+1)+length(m[1,])-1)
colnames(n)=(max(as.numeric(colnames(m)))+1):((max(as.numeric(colnames(m)))+1)+length(n[1,])-1)
colnames(o)=(max(as.numeric(colnames(n)))+1):((max(as.numeric(colnames(n)))+1)+length(o[1,])-1)
colnames(p)=(max(as.numeric(colnames(o)))+1):((max(as.numeric(colnames(o)))+1)+length(p[1,])-1)
colnames(q)=(max(as.numeric(colnames(p)))+1):((max(as.numeric(colnames(p)))+1)+length(q[1,])-1)
colnames(r)=(max(as.numeric(colnames(q)))+1):((max(as.numeric(colnames(q)))+1)+length(r[1,])-1)
sptesta=cbind(a,b,c,d,e,f)
sptestb=cbind(g,h,i,j,k,l)
sptestc=cbind(m,n,o,p,q,r)
sptest=rbind(sptesta,sptestb,sptestc)
#
#
#
# str(sptest)
# str(globalmatrix)
#
# interm=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13)[1]) & as.numeric(substr(rownames(globalmatrix),15,16)) %in% ((6*0)+1):(6*(0+1)) ),])
# if (length(interm[,1])==6){
# # I=interm[1,] #cbind(a=interm[1,], b=interm[2,], c=interm[3,], d=interm[4,], e=interm[5,], f=interm[6,])
# # for(k in 1:6){
# # rownames(interm)[1]=paste(substr(rownames(interm)[1],1,13),substr(rownames(interm)[1],18,18),j, sep="")
# I=cbind(interm[1,], interm[2,], interm[3,], interm[4,], interm[5,], interm[6,])
# spb=I
# }
#
#
# for (j in 1:2){
# interm=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13)[1]) & as.numeric(substr(rownames(globalmatrix),15,16)) %in% ((6*j)+1):(6*(j+1)) ),])
# if (length(interm[,1])==6){
# # I=interm[1,] #cbind(a=interm[1,], b=interm[2,], c=interm[3,], d=interm[4,], e=interm[5,], f=interm[6,])
# # for(k in 1:6){
# # rownames(interm)[1]=paste(substr(rownames(interm)[1],1,13),substr(rownames(interm)[1],18,18),j, sep="")
# I=cbind(interm[1,], interm[2,], interm[3,], interm[4,], interm[5,], interm[6,])
# spb=rbind(spb,I)
# }
# }
#
# for (i in 2:length(unique(substr(rownames(globalmatrix),1,13)))) {
# for (j in 0:2){
# interm=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13)[i]) & as.numeric(substr(rownames(globalmatrix),15,16)) %in% ((6*j)+1):(6*(j+1)) ),])
# print(length(interm[,1]))
# if (length(interm[,1])==6){ #6
# I=cbind(interm[1,], interm[2,], interm[3,], interm[4,], interm[5,], interm[6,])
# spb=rbind(spb,I)
# }
# }
# }
# str(spb) #Trop de lignes, non ?
# # L[which(L!=6)]
# # which(L!=6)
#
#
# interm=sp[which(paste(substr(rownames(sp),1,13),sp$souche)==unique(paste(substr(rownames(sp),1,13),sp$souche))[10]),]
#
# length(interm[,1])
#
#
globalmatrix2=sptest
globalmatrix2=globalmatrix2[complete.cases(globalmatrix2),]
str(globalmatrix)
str(globalmatrix2)
brb="C:/Users/avitvale/Documents/Test/"
save(globalmatrix2, file=paste(brb,"globalmatrix2",sep=""))
print(length(globalmatrix2))
# write.table(globalmatrix, file=paste(brb,"globalmatrix.csv",sep=""),sep=";", quote=FALSE)
setwd("C:/Users/avitvale/Documents/signeG")
### END ###
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## COMPRESSION DES SPECTRES EN UNE MATRICE ##
# nettoyage des variables de l'espace de travail
rm(list = ls())
source('C:/Users/avitvale/Documents/Script_R/SIGNE_load.R') ##### N'arrive pas à trouver le chemin "normal (dans signeG), comprends pas pourquoi
source('C:/Users/avitvale/Documents/Script_R/adj_asd.R')
source('C:/Users/avitvale/Documents/Script_R/asd_read.R')
# #création de la matrice qui rassemble tous les dossiers:
globalmatrix=matrix(ncol=2072)
setwd("C:/Users/avitvale/Documents/SIGNE")
for (a in 2017:2019){
setwd("C:/Users/avitvale/Documents/SIGNE") #Mettre ici le chemin d'accès au dossier contenant les spectres
setwd(as.character(a)) #On balaie les trois dossiers année
for (n in 1:length(dir())){
if ((dir()[n])=="Aude" | (dir()[n])=="Beaujolais" | (dir()[n])=="GDRautre" |(dir()[n])=="GDR96"){
lieu=substr(dir()[n],1,1) #On attribue au spectre un identifiant lieu selon sa parcelle d'origine : A, B, G ou g
if ((dir()[n])=="GDRautre"){
lieu='g'
}
setwd(as.character(dir()[n])) #On entre dans le sous-dossier.
for (m in 1:length(dir())){
if(substr(dir()[m],9,9)=="P"){ #on ne s'intéresse qu'au mesures effectuées en suivant la modalité P
em=paste(dir()[m], sep="")
w=SIGNE_load(em)
rownames(w)=paste(dir()[m],rownames(w),lieu) #On ajoute l'identifiant lieu au nom de chaque spectre
globalmatrix=rbind(globalmatrix, w)
}
}
setwd("../")
}
}
}
globalmatrix=globalmatrix[complete.cases(globalmatrix),]
#str(globalmatrix)
#Filtrage des noms non standardisés
iout=which(nchar(rownames(globalmatrix))>18)
# rownames(globalmatrix[iout,])
# unique(rownames(globalmatrix[which(substr(rownames(globalmatrix),1,8)=="20170612"),]))
globalmatrix <- globalmatrix[-iout,]
## Filtrage des spectres aberrants #Tous les spectres aberrants sont-ils filtrés par ce moyen ?
globalmatrix=globalmatrix[globalmatrix[,500]>0.6,] #Actuellement, 33 spectres jugés aberrants filtrés ici. (Dont 5 qui ne font pas partie de nos 10 clones étudiés..?)
globalmatrix=globalmatrix[globalmatrix[,1]<0.2,]
globalmatrix=globalmatrix[globalmatrix[,2000]<0.25,]
## Ajustement des sauts de detecteur (Montpellier: sauts ?? 1000 (651 eme l.o.) et 1800 (1451))
########globalmatrix=adj_asd(globalmatrix,c(602,1402))
## Reduction des variables (extremites bruitees)
globalmatrix=globalmatrix[,seq(51,ncol(globalmatrix)-30,1)]
# ###Ajout du cepage au nom de la ligne. Retire aussi les cépages/clones qui ne sont pas les 3/10 notres.
# ##Filtre en fonction du cepage
# titre=rownames(globalmatrix)
#
# ya=(substr(titre,11,13))== "015"
# yb=(substr(titre,11,13))== "169"
# yc=(substr(titre,11,13))== "685"
#
# yd=(substr(titre,11,13))== "222"
# ye=(substr(titre,11,13))== "509"
# yf=(substr(titre,11,13))== "787"
#
# yg=(substr(titre,11,13))== "471"
# yh=(substr(titre,11,13))== "525"
# yi=(substr(titre,11,13))== "747"
# yj=(substr(titre,11,13))== "877"
#
# ##Separation en 3 matrices
# spa=globalmatrix[ya,]
# spb=globalmatrix[yb,]
# spc=globalmatrix[yc,]
# spd=globalmatrix[yd,]
# spe=globalmatrix[ye,]
# spf=globalmatrix[yf,]
# spg=globalmatrix[yg,]
# sph=globalmatrix[yh,]
# spi=globalmatrix[yi,]
# spj=globalmatrix[yj,]
#
# ##Rajoute le nom du cepage au nom de la ligne à la place de P/T/N
# substr(rownames(spa),9,9)="C"
# substr(rownames(spb),9,9)="C"
# substr(rownames(spc),9,9)="C"
#
# substr(rownames(spd),9,9)="G"
# substr(rownames(spe),9,9)="G"
# substr(rownames(spf),9,9)="G"
#
# substr(rownames(spg),9,9)="S"
# substr(rownames(sph),9,9)="S"
# substr(rownames(spi),9,9)="S"
# substr(rownames(spj),9,9)="S"
#
# ##Recombine les 3 matrices pour reformer sp
# globalmatrix=rbind(spa,spb,spc,spd,spe,spf,spg,sph,spi,spj)
#Cette méthode est équivalente à ce qui précède, simplement les spectres dans la globalmatrix ne sont pas dans le même ordre.
for (i in 1:length(globalmatrix[,1])){
if (substr(rownames(globalmatrix)[i],11,13)=="015" | substr(rownames(globalmatrix)[i],11,13)=="169" | substr(rownames(globalmatrix)[i],11,13)=="685"){
substr(rownames(globalmatrix)[i],9,9)="C"
}
else if (substr(rownames(globalmatrix)[i],11,13)=="222" | substr(rownames(globalmatrix)[i],11,13)=="509" | substr(rownames(globalmatrix)[i],11,13)=="787"){
substr(rownames(globalmatrix)[i],9,9)="G"
}
else if (substr(rownames(globalmatrix)[i],11,13)=="471" | substr(rownames(globalmatrix)[i],11,13)=="525" | substr(rownames(globalmatrix)[i],11,13)=="747" | substr(rownames(globalmatrix)[i],11,13)=="877"){
substr(rownames(globalmatrix)[i],9,9)="S"
}
else {
substr(rownames(globalmatrix)[i],9,9)="A"
}
}
iout=which(substr(rownames(globalmatrix),9,9)=="A")
globalmatrix <- globalmatrix[-iout,]
str(globalmatrix)
a=matrix(ncol=1992)
b=matrix(ncol=1992)
c=matrix(ncol=1992)
d=matrix(ncol=1992)
e=matrix(ncol=1992)
f=matrix(ncol=1992)
g=matrix(ncol=1992)
h=matrix(ncol=1992)
i=matrix(ncol=1992)
j=matrix(ncol=1992)
k=matrix(ncol=1992)
l=matrix(ncol=1992)
m=matrix(ncol=1992)
n=matrix(ncol=1992)
o=matrix(ncol=1992)
p=matrix(ncol=1992)
q=matrix(ncol=1992)
r=matrix(ncol=1992)
colnames(a)=449:2440
colnames(b)=449:2440
colnames(c)=449:2440
colnames(d)=449:2440
colnames(e)=449:2440
colnames(f)=449:2440
colnames(g)=449:2440
colnames(h)=449:2440
colnames(i)=449:2440
colnames(j)=449:2440
colnames(k)=449:2440
colnames(l)=449:2440
colnames(m)=449:2440
colnames(n)=449:2440
colnames(o)=449:2440
colnames(p)=449:2440
colnames(q)=449:2440
colnames(r)=449:2440
# interm=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13)[1])),])
# if (length(interm[,1])==18){
# a=rbind(a,interm[1,])
# rownames(a)[length(a[,1])]=paste(substr(rownames(interm)[length(a[,1])],1,13),"-00 ", substr(rownames(interm)[length(a[,1])],18,18),1, sep="")
# # b=rbind(b,interm[2,])
# # c=rbind(c,interm[3,])
# # d=rbind(d,interm[4,])
# # e=rbind(e,interm[5,])
# # f=rbind(f,interm[6,])
# # g=rbind(g,interm[7,])
# # h=rbind(h,interm[8,])
# # i=rbind(i,interm[9,])
# # j=rbind(j,interm[10,])
# # k=rbind(k,interm[11,])
# # l=rbind(l,interm[12,])
# # m=rbind(m,interm[13,])
# # n=rbind(n,interm[14,])
# # o=rbind(o,interm[15,])
# # p=rbind(p,interm[16,])
# # q=rbind(q,interm[17,])
# # r=rbind(r,interm[18,])
# }
for (z in 1:length(unique(substr(rownames(globalmatrix),1,13)))) {
interm=globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13))[z]),]
# truc1=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13))[1]),])
# truc2=globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13))[1]),]
if (length(interm[,1])==18){
a=rbind(a,interm[1,])
K=as.character(paste(substr(rownames(interm)[1],1,13),"-01 ", substr(rownames(interm)[1],18,18), sep=""))
rownames(a)[length(a[,1])]=K
b=rbind(b,interm[2,])
K=as.character(paste(substr(rownames(interm)[2],1,13),"-01 ", substr(rownames(interm)[2],18,18), sep=""))
rownames(b)[length(b[,1])]=K
c=rbind(c,interm[3,])
K=as.character(paste(substr(rownames(interm)[3],1,13),"-01 ", substr(rownames(interm)[3],18,18), sep=""))
rownames(c)[length(c[,1])]=K
d=rbind(d,interm[4,])
K=as.character(paste(substr(rownames(interm)[4],1,13),"-01 ", substr(rownames(interm)[4],18,18), sep=""))
rownames(d)[length(d[,1])]=K
e=rbind(e,interm[5,])
K=as.character(paste(substr(rownames(interm)[5],1,13),"-01 ", substr(rownames(interm)[5],18,18), sep=""))
rownames(e)[length(e[,1])]=K
f=rbind(f,interm[6,])
K=as.character(paste(substr(rownames(interm)[6],1,13),"-01 ", substr(rownames(interm)[6],18,18), sep=""))
rownames(f)[length(f[,1])]=K
g=rbind(g,interm[7,])
K=as.character(paste(substr(rownames(interm)[7],1,13),"-07 ", substr(rownames(interm)[7],18,18), sep=""))
rownames(g)[length(g[,1])]=K
h=rbind(h,interm[8,])
K=as.character(paste(substr(rownames(interm)[8],1,13),"-07 ", substr(rownames(interm)[8],18,18), sep=""))
rownames(h)[length(h[,1])]=K
i=rbind(i,interm[9,])
K=as.character(paste(substr(rownames(interm)[9],1,13),"-07 ", substr(rownames(interm)[9],18,18), sep=""))
rownames(i)[length(i[,1])]=K
j=rbind(j,interm[10,])
K=as.character(paste(substr(rownames(interm)[10],1,13),"-07 ", substr(rownames(interm)[10],18,18), sep=""))
rownames(j)[length(j[,1])]=K
k=rbind(k,interm[11,])
K=as.character(paste(substr(rownames(interm)[11],1,13),"-07 ", substr(rownames(interm)[11],18,18), sep=""))
rownames(k)[length(k[,1])]=K
l=rbind(l,interm[12,])
K=as.character(paste(substr(rownames(interm)[12],1,13),"-07 ", substr(rownames(interm)[12],18,18), sep=""))
rownames(l)[length(l[,1])]=K
m=rbind(m,interm[13,])
K=as.character(paste(substr(rownames(interm)[13],1,13),"-13 ", substr(rownames(interm)[13],18,18), sep=""))
rownames(m)[length(m[,1])]=K
n=rbind(n,interm[14,])
K=as.character(paste(substr(rownames(interm)[14],1,13),"-13 ", substr(rownames(interm)[14],18,18), sep=""))
rownames(n)[length(n[,1])]=K
o=rbind(o,interm[15,])
K=as.character(paste(substr(rownames(interm)[15],1,13),"-13 ", substr(rownames(interm)[15],18,18), sep=""))
rownames(o)[length(o[,1])]=K
p=rbind(p,interm[16,])
K=as.character(paste(substr(rownames(interm)[16],1,13),"-13 ", substr(rownames(interm)[16],18,18), sep=""))
rownames(p)[length(p[,1])]=K
q=rbind(q,interm[17,])
K=as.character(paste(substr(rownames(interm)[17],1,13),"-13 ", substr(rownames(interm)[17],18,18), sep=""))
rownames(q)[length(q[,1])]=K
r=rbind(r,interm[18,])
K=as.character(paste(substr(rownames(interm)[18],1,13),"-13 ", substr(rownames(interm)[18],18,18), sep=""))
rownames(r)[length(r[,1])]=K
}
}
colnames(b)=(max(as.numeric(colnames(a)))+1):((max(as.numeric(colnames(a)))+1)+length(b[1,])-1)
colnames(c)=(max(as.numeric(colnames(b)))+1):((max(as.numeric(colnames(b)))+1)+length(c[1,])-1)
colnames(d)=(max(as.numeric(colnames(c)))+1):((max(as.numeric(colnames(c)))+1)+length(d[1,])-1)
colnames(e)=(max(as.numeric(colnames(d)))+1):((max(as.numeric(colnames(d)))+1)+length(e[1,])-1)
colnames(f)=(max(as.numeric(colnames(e)))+1):((max(as.numeric(colnames(e)))+1)+length(f[1,])-1)
#colnames(g)=(max(as.numeric(colnames(f)))+1):((max(as.numeric(colnames(f)))+1)+length(g[1,])-1)
colnames(h)=(max(as.numeric(colnames(g)))+1):((max(as.numeric(colnames(g)))+1)+length(h[1,])-1)
colnames(i)=(max(as.numeric(colnames(h)))+1):((max(as.numeric(colnames(h)))+1)+length(i[1,])-1)
colnames(j)=(max(as.numeric(colnames(i)))+1):((max(as.numeric(colnames(i)))+1)+length(j[1,])-1)
colnames(k)=(max(as.numeric(colnames(j)))+1):((max(as.numeric(colnames(j)))+1)+length(k[1,])-1)
colnames(l)=(max(as.numeric(colnames(k)))+1):((max(as.numeric(colnames(k)))+1)+length(l[1,])-1)
#colnames(m)=(max(as.numeric(colnames(l)))+1):((max(as.numeric(colnames(l)))+1)+length(m[1,])-1)
colnames(n)=(max(as.numeric(colnames(m)))+1):((max(as.numeric(colnames(m)))+1)+length(n[1,])-1)
colnames(o)=(max(as.numeric(colnames(n)))+1):((max(as.numeric(colnames(n)))+1)+length(o[1,])-1)
colnames(p)=(max(as.numeric(colnames(o)))+1):((max(as.numeric(colnames(o)))+1)+length(p[1,])-1)
colnames(q)=(max(as.numeric(colnames(p)))+1):((max(as.numeric(colnames(p)))+1)+length(q[1,])-1)
colnames(r)=(max(as.numeric(colnames(q)))+1):((max(as.numeric(colnames(q)))+1)+length(r[1,])-1)
sptesta=cbind(a,b,c,d,e,f)
sptestb=cbind(g,h,i,j,k,l)
sptestc=cbind(m,n,o,p,q,r)
sptest=rbind(sptesta,sptestb,sptestc)
#
#
#
# str(sptest)
# str(globalmatrix)
#
# interm=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13)[1]) & as.numeric(substr(rownames(globalmatrix),15,16)) %in% ((6*0)+1):(6*(0+1)) ),])
# if (length(interm[,1])==6){
# # I=interm[1,] #cbind(a=interm[1,], b=interm[2,], c=interm[3,], d=interm[4,], e=interm[5,], f=interm[6,])
# # for(k in 1:6){
# # rownames(interm)[1]=paste(substr(rownames(interm)[1],1,13),substr(rownames(interm)[1],18,18),j, sep="")
# I=cbind(interm[1,], interm[2,], interm[3,], interm[4,], interm[5,], interm[6,])
# spb=I
# }
#
#
# for (j in 1:2){
# interm=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13)[1]) & as.numeric(substr(rownames(globalmatrix),15,16)) %in% ((6*j)+1):(6*(j+1)) ),])
# if (length(interm[,1])==6){
# # I=interm[1,] #cbind(a=interm[1,], b=interm[2,], c=interm[3,], d=interm[4,], e=interm[5,], f=interm[6,])
# # for(k in 1:6){
# # rownames(interm)[1]=paste(substr(rownames(interm)[1],1,13),substr(rownames(interm)[1],18,18),j, sep="")
# I=cbind(interm[1,], interm[2,], interm[3,], interm[4,], interm[5,], interm[6,])
# spb=rbind(spb,I)
# }
# }
#
# for (i in 2:length(unique(substr(rownames(globalmatrix),1,13)))) {
# for (j in 0:2){
# interm=as.data.frame(globalmatrix[which(substr(rownames(globalmatrix),1,13)==unique(substr(rownames(globalmatrix),1,13)[i]) & as.numeric(substr(rownames(globalmatrix),15,16)) %in% ((6*j)+1):(6*(j+1)) ),])
# print(length(interm[,1]))
# if (length(interm[,1])==6){ #6
# I=cbind(interm[1,], interm[2,], interm[3,], interm[4,], interm[5,], interm[6,])
# spb=rbind(spb,I)
# }
# }
# }
# str(spb) #Trop de lignes, non ?
# # L[which(L!=6)]
# # which(L!=6)
#
#
# interm=sp[which(paste(substr(rownames(sp),1,13),sp$souche)==unique(paste(substr(rownames(sp),1,13),sp$souche))[10]),]
#
# length(interm[,1])
#
#
globalmatrix2=sptest
globalmatrix2=globalmatrix2[complete.cases(globalmatrix2),]
str(globalmatrix)
str(globalmatrix2)
brb="C:/Users/avitvale/Documents/Test/"
save(globalmatrix2, file=paste(brb,"globalmatrix2",sep=""))
print(length(globalmatrix2))
# write.table(globalmatrix, file=paste(brb,"globalmatrix.csv",sep=""),sep=";", quote=FALSE)
setwd("C:/Users/avitvale/Documents/signeG")
### END ###
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