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@xitong
xitong committed Dec 9, 2022
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97 changes: 97 additions & 0 deletions by_date2_V2.R
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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))
}
}

258 changes: 258 additions & 0 deletions by_date3_LDC_v0716.R
@@ -0,0 +1,258 @@
by_date3<-function(file,gal4,light,length,cycle,drug,yrange,namecolor,legend=0){
setwd(sprintf("~/Dropbox/lab/data sheet/%s/date",file))
source('~/Dropbox/R/filter_na.R')
source('~/Dropbox/R/smooth.R')
name=list.files()
lgd=c("LNd","lLNv","DN1","DN3","sLNv","fifth_sLNv")
LNd=lLNv=DN1=DN3=sLNv=fifth_sLNv=list()
if(missing(length)){length=12}
if(missing(cycle)){cycle=T}
#par(cex=1)
if(is.numeric(gal4)){
#cell=seq(1,gal4)
cell=gal4
cells=6}

else{
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=="pdfrB_pdf80"){cell=c(1,6)
cells=6}
if(gal4=="929"){cell=c(1,2)
cells=5}
if(gal4=="TH"){cell=c(1,2,3,4,5)
cells=5}
if(gal4=="THC"){cell=c(1,2)
cells=5}
if(gal4=="THD"){cell=c(3,4,5)
cells=5}
}





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 cell){
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]
}}
#for (j in 1:dim(a)[1]){ff[j,i]=a[j,(i-1)*3+2]}
#ff[,i]=filter_na_2(ff[,i],7)
if(cycle){
ff[,i]=filter_na_2(ff[,i],7)
ff[,i]=filter(ff[,i], filter=rep(1/7, 7),sides=2,circular = T)
#ff1=filter_na_2(ff[,i],7)
# if(!is.na(sum(ff1))){
# ff[,i]=filter(ff1, filter=rep(1/7, 7),sides=2,circular = TRUE)}
# else{
# ff[,i]=filter(ff[,i], filter=rep(1/7, 7),sides=2,circular = F)
# ff[,i]=filter(ff[,i], filter=rep(1/7, 7),sides=2,circular = F)
# }
}
if(!cycle){
ff[,i]=filter_na_2(ff[,i],1)}
#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 cell){
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],7)
ff[,i]=filter(ff[,i], filter=rep(1/7, 7),sides=2,circular = TRUE)
}
}
}
if(!cycle){
ff=smooth(ff)
ff=smooth(ff)
}
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"||gal4==6){
fifth_sLNv[[length(fifth_sLNv)+1]]=ff[,6]
}
}

############photoperiod
off=length
if (file=="LD"){off=16}
if (file=="SD"){off=8}

################################################################
lgd=c("LNd","lLNv","DN1","DN3","sLNv","fifth_sLNv")
color=c("blue","red","green","magenta","orange","cyan")
t=c(0:143)/6
library("matrixStats")
meanf=stdf=matrix(,144,6)
change=area=wide1=wide2=matrix(,length(LNd),6)

for (k in cell){
ff=get(lgd[k])
f=matrix(,144,length(ff))
rep=0
for (j in 1:length(ff)){
#f[,j]=ff[[j]]
#normalize to 0-100
#f[,j]=(ff[[j]]-min(ff[[j]]))/(max(ff[[j]])-min(ff[[j]]))
#df/fmax
if(!sum(ff[[j]],na.rm=T)==0){
if(cycle){
f[,j]=(ff[[j]]-min(ff[[j]],na.rm=TRUE))/min(ff[[j]],na.rm=TRUE)}
#f[,j]=(ff[[j]]-min(ff[[j]],na.rm=TRUE))/max(ff[[j]],na.rm=TRUE)}
#f[,j]=(ff[[j]]-min(ff[[j]],na.rm=TRUE))/mean(ff[[j]],na.rm=TRUE)}
#f[,j]=(ff[[j]]-mean(ff[[j]],na.rm=TRUE))/sd(ff[[j]],na.rm=TRUE)}
if(!cycle){
f[,j]=(ff[[j]]-ff[[j]][1])/max(ff[[j]],na.rm=TRUE)}

change[j,k]=max(ff[[j]],na.rm=TRUE)-min(ff[[j]],na.rm=TRUE)

}
#f[,j]=(ff[[j]]-min(ff[[j]],na.rm=TRUE))/max(ff[[j]],na.rm=TRUE)
#f[,i]=filter(f[,i], filter=rep(1/5, 5),sides=2,circular = TRUE)
#f[,j]=(ff[[j]]-min(ff[[j]]))
##df/f0
#f[,j]=(ff[[j]]-ff[[j]][1])/ff[[j]][1]
#f[,j]=(ff[[j]]-min(ff[[j]]))/mean(ff[[j]])
if(!is.na(sum(f[,j]))){
rep=rep+1
wide1[j,k]=which.min(abs(max(f[,j])/2- f[1:which.max(f[,j]),j]))
wide2[j,k]=which.min(abs(max(f[,j])/2- f[which.max(f[,j]):144,j]))+which.max(f[,j])
}
change[j,k]=(max(f[,j])-min(f[,j]))
area[j,k]=sum(f[,j])
}
meanf[,k]=rowMeans(f,na.rm=TRUE)
stdf[,k]=rowSds(f,na.rm=TRUE)/(sqrt(rep))

yy=range(f,na.rm = TRUE)
par(xpd=TRUE,mai=c(1,1,1,2),cex=1)
# plot(1,type='n',xlim=range(t),ylim=yy,xaxp=c(0,24,6),xlab='ZT/h',ylab='dF/F',main=lgd[k])
# polygon(c(off,24,24,off),c(yy[1],yy[1],yy[2],yy[2]),col="gray",border=NA)
# matlines(t,f,type="l",lty=1,col=rainbow(length(name)))
#
#

par(xpd=TRUE)
par(mai=c(1,1,1,2))
par(oma=c(0,0,0,0))
plot(1,type='n',xlim=range(t),ylim=yy,xaxp=c(0,24,6),xlab="Circadian Time (h)",ylab='ΔF/F',mgp=c(1.5,.5,0))
polygon(c(off,24,24,off),c(yy[1],yy[1],yy[2],yy[2]),col="gray",border=NA)
matlines(t,f,type="l",lty=1,col=rainbow(length(name)))
legend(max(t)+1.5,max(yy)-k/30,legend=name,col=rainbow(length(name)),lty=1,cex = 0.7,,bty="n")

}

###############plot################################
lgd=c("LNd","l-LNv","DN1","DN3","s-LNv","5th-sLNv")
if(gal4=="pdfrB"||gal4=="pdfrB_pdf80"){
lgd=c("PDFR+LNd","l-LNv","DN1","DN3","s-LNv","5th-sLNv")}

if(is.numeric(gal4)||grepl("TH",gal4)){
color=c("gold","orchid2","deepskyblue2","tomato","seagreen2","deepskyblue2")
lgd=c("PAL","PAM","PPL1","PPM1","PPM3")
}
if(!missing(namecolor)){color=namecolor}
color_transparent <- adjustcolor(color, alpha.f = 0.1)
bglight <- adjustcolor("yellow", alpha.f = 0.2)

if(file=="PER_LDC"||grepl("per0",file)){yy=c(0,0.4)}

if(missing(yrange)){yy=c(min(meanf,na.rm=TRUE)-mean(stdf,na.rm=TRUE),max(meanf,na.rm=TRUE)+max(stdf,na.rm=TRUE))}
else{yy=yrange}

par(xpd=TRUE,mai=c(1,1,1,2.5))
#meanf=filter(meanf, filter=rep(1/7, 7),sides=2,circular = TRUE)
plot(1,type='n',xlim=range(t),ylim=yy,xaxp=c(0,24,6),xlab="",ylab='ΔF/F',mgp=c(1.5,.5,0))
if(missing(light)){
polygon(c(off,24,24,off),c(yy[1],yy[1],yy[2],yy[2]),col="gray",border=NA)
polygon(c(off,0,0,off),c(yy[1],yy[1],yy[2],yy[2]),col=gray(0.95),border=NA)
light=0
title(xlab="Circadian Time (h)",line=1.5)
}
if(light=="LD"){
polygon(c(off,24,24,off),c(yy[1],yy[1],yy[2],yy[2]),col="gray",border=NA)
polygon(c(off,0,0,off),c(yy[1],yy[1],yy[2],yy[2]),col=bglight,border=NA)
title(xlab="Zeitgeber Time (h)",line=1.5)
}
if(light=="DD"){
polygon(c(0,24,24,0),c(yy[1],yy[1],yy[2],yy[2]),col="gray",border=NA)
title(xlab="Circadian Time (h)",line=1.5)
}


#############lines

for (k in cell){
polygon(c(t, rev(t)), c(stdf[,k]+meanf[,k], rev(-stdf[,k]+meanf[,k])),col=color_transparent[k], border = NA)
lines(t,meanf[,k],col=color[k],lwd=3)
lines(t,stdf[,k]+meanf[,k],col=color[k],lwd=0.25)
lines(t,-stdf[,k]+meanf[,k],col=color[k],lwd=0.25)
#legend(max(t)+1.5,max(yy)-k/30,legend=lgd[k],col=color[k],lty=1,cex = 0.7,bty="n")
}
if(legend){
#legend(max(t)+1,max(yy),legend=c("",""),col=color[cell],lty=1,lwd=6,cex = 1,bty="n")
legend(max(t)+1,max(yy),legend=lgd[cell],col=color[cell],lty=1,lwd=6,cex = 1.75,bty="n")
}
# if(!missing(namecolor)){
# legend(max(t)+1,max(yy),legend=c("",""),col=namecolor,lty=1,lwd=6,cex = 1,bty="n")
# }
if(!missing(drug)){polygon(c(drug,drug+0.2,drug+0.2,drug),c(yy[1],yy[1],yy[2],yy[2]),col="RED",border=NA)}

#########summary
name=amplitude=sem.amplitude=width=sem.width=mean.area=sem.area=n=matrix(,6,1)
sum=data.frame(name,amplitude,sem.amplitude,width,sem.width,mean.area,sem.area,n)

for(i in cell){
sum$name[i]=lgd[i]
sum$n[i]=length(change[,i])-sum(is.na(change[,i]))
sum$amplitude[i]=signif(mean(change[,i],na.rm=T),2)
sum$sem.amplitude[i]=signif(sd(change[,i],na.rm=T)/sqrt(sum$n[i]),2)
w=(wide1[,i]-wide2[,i])/6
w=abs(w)
sum$width[i]=signif(mean(w,na.rm=T),2)
sum$sem.width[i]=signif(sd(w,na.rm=T)/sqrt(sum$n[i]),2)
sum$mean.area[i]=signif(mean(area[,i],na.rm=T),2)
sum$sem.area[i]=signif(sd(area[,i],na.rm=T)/sqrt(sum$n[i]),2)

}
write.csv(sum,file=sprintf("~/Dropbox/lab/data sheet/%s/summary_wave.csv",file))


# write.csv(change,file=sprintf("~/Dropbox/lab/data sheet/%s/change.csv",file))
# write.csv(list(wide1,wide2),file=sprintf("~/Dropbox/lab/data sheet/%s/width.csv",file))
# write.csv(area,file=sprintf("~/Dropbox/lab/data sheet/%s/area.csv",file))
return(meanf)
}

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