by_date2_V2.R

by_date2<-function(file,gal4){
  setwd(sprintf("~/Dropbox/lab/data sheet/%s/date",file))
  source('~/Dropbox/R/filter_na.R')
  if(gal4=="tim"){cell=c(3,4,1,2,5)
  cells=5}
  if(gal4=="pdf"){cell=c(2,5)
  cells=5}
  if(gal4=="pdfrB"){cell=c(1,6,5)
  cells=6}
  if(gal4=="pdf80"){cell=c(3,4,1)
  cells=5}
  if(gal4=="645"){cell=c(3,4,1,5)
  cells=5}
  if(gal4=="681"){cell=c(3,4,1,2)
  cells=5}
  if(gal4=="pdfrB_pdf80"){cell=c(1,6)
  cells=6}
  if(gal4=="929"){cell=c(2)
  cells=5}
  
  if(is.numeric(gal4)){
    cell=seq(1,gal4)
    cells=5}

  
  name=list.files()
  
  LNd=lLNv=DN1=DN3=sLNv=fifth_sLNv=list()
  for (k in 1:length(name)){  
    a=read.csv(name[k],header=TRUE)
    time=a[,1]
    
    ff=matrix(,144,cells)
    t=as.integer(144-time[1]/(24/144))
    #row states
    if(grepl("Row",name[k])){
      for (i in 1:cells){ if (length(a)>(i-1)*3+2){
        if(sum(a[,(i-1)*3+2],na.rm=TRUE)!=0){
          for (j in 1:t){
            ff[j+144-t,i]=a[j,(i-1)*3+2]
          }
          if(t<144){
            for (j in (t+1):length(time)){
              ff[j-t,i]=a[j,(i-1)*3+2]
            }}
          ff[,i]=filter_na_2(ff[,i])
          ff[,i]=filter(ff[,i], filter=rep(1/7, 7),sides=2,circular = TRUE)
          ff[,i]=((ff[,i])-min(ff[,i],na.rm = TRUE))/(max(ff[,i],na.rm = TRUE)-min(ff[,i],na.rm = TRUE))*100
        }    
      }}
    }
    #by_date
    if(!grepl("Row",name[k])){
      for (i in 1:cells){
        if(sum(a[,i+1],na.rm=TRUE)!=0){
          for (j in 1:t){
            ff[j+144-t,i]=a[j,i+1]
          }
          if(t<144){
            for (j in (t+1):length(time)){
              ff[j-t,i]=a[j,i+1]
            }
          }
          ff[,i]=filter_na_2(ff[,i])
          ff[,i]=filter(ff[,i], filter=rep(1/7, 7),sides=2,circular = TRUE)
          ff[,i]=((ff[,i])-min(ff[,i],na.rm = TRUE))/(max(ff[,i],na.rm = TRUE)-min(ff[,i],na.rm = TRUE))*100
        }    
      }
    }
  
  
    LNd[[length(LNd)+1]]=ff[,1]
    lLNv[[length(lLNv)+1]]=ff[,2]
    DN1[[length(DN1)+1]]=ff[,3]
    DN3[[length(DN3)+1]]=ff[,4]
    sLNv[[length(sLNv)+1]]=ff[,5]
    
    if(gal4=="pdfrB"||gal4=="pdfrB_pdf80"){
      fifth_sLNv[[length(fifth_sLNv)+1]]=ff[,6]    
    }
    
    
  }
  names(LNd) <- c("LNd")
  names(lLNv) <- c("lLNv") 
  names(DN1) <- c("DN1")
  names(DN3) <- c("DN3")
  names(sLNv) <- c("sLNv") 
  
  save(LNd,lLNv,sLNv,DN1,DN3,file=sprintf("~/Dropbox/lab/data sheet/%s/%s_celltype.RData",file,file))
  
  if(gal4=="pdfrB"||gal4=="pdfrB_pdf80"){
    names(fifth_sLNv) <- c("fifth_sLNv") 
    save(LNd,lLNv,sLNv,DN1,DN3,fifth_sLNv,file=sprintf("~/Dropbox/lab/data sheet/%s/%s_celltype.RData",file,file))
  }
}