# Lobster_Lesion_CaH_080613.R
filnam="Lobster_CaHonJun13.csv"
ZZ<- read.csv(filnam, skip=18)
attach(ZZ)
print(names(ZZ))
Min_From<-ZZ[,1]
X_microns<-ZZ[,2]
Y_microns<-ZZ[,3]
Z_microns<-ZZ[,4]

quartz(width=18, height=6)
plot(c(min(Min_From),max(Min_From)), c(min(Y_microns),max(X_microns)), 
     typ='n', 
     main=paste(filnam,"Position, X=red, Y=green, Z=blue"),
     xlab="time (min)",
     ylab="position um")
points(Min_From, Z_microns, col='blue', pch=20)
points(Min_From, Y_microns, col='green', pch=20)
points(Min_From, X_microns, col='red', pch=20)

browser()
quartz(width=18, height=6)
plot(X_microns, Y_microns, main=paste(filnam,"Y_microns vs X_microns")) 
browser()
quartz(width=8, height=6)

## AvggradHuV,AvgGradCauV
batch1<- 1:123 
plot(c(min(X_microns[batch1]), max(X_microns[batch1])), c(-100,100), typ='n', 
      main=paste(filnam,"uV vs X_microns, H(black), Ca(red), batch-1")) 
points(X_microns[batch1], AvggradHuV[batch1], col='black')
points(X_microns[batch1], AvgGradCauV[batch1], col='red')

browser()
quartz(width=5.5, height=6)
plot(X_microns[batch1], Y_microns[batch1], main=paste(filnam,"batch 1 positions"))

browser()
quartz(width=8, height=6)
## AvggradHuV,AvgGradCauV
batch2<- 145:225 
batch2above<-batch2[1:11]
batch2zero<-batch2[12:81]

plot(c(min(Y_microns[batch2]), max(Y_microns[batch2])), c(-100,100),  
      typ='n',
      main=paste(filnam,"uV vs Y_microns, H(black), Ca(red), batch-2")) 
points(Y_microns[batch2zero], AvggradHuV[batch2zero], col='black')
points(Y_microns[batch2zero], AvgGradCauV[batch2zero], col='red')
text(-50, 25, "Center")
text(948, -90, "Out")
text(748, -90, "Border")

browser()
quartz(width=5, height=6)
plot(X_microns[batch2zero], Y_microns[batch2zero], main=paste(filnam,"batch 2 positions"))
browser()

detach(ZZ)