##################################################
# Function for Mapping 24/48/96 to 384 Well Plates 
##################################################

# (1) 384 Plate 
P384 <-  matrix(paste(rep(1,384), matrix(LETTERS[1:16],16,24, byrow=F), matrix(1:24,16,24, byrow=T), sep=""),16,24, dimnames = list(LETTERS[1:16], 1:24))

# (2) 384_4x96 Mapping Plate 
P96_1 <- matrix(paste(rep(1,96), matrix(LETTERS[1:8],8,12, byrow=F), matrix(1:12,8,12, byrow=T), sep=""),8,12, dimnames = list(LETTERS[1:8], 1:12))
P96_2 <- matrix(paste(rep(2,96), matrix(LETTERS[1:8],8,12, byrow=F), matrix(1:12,8,12, byrow=T), sep=""),8,12, dimnames = list(LETTERS[1:8], 1:12))
P96_3 <- matrix(paste(rep(3,96), matrix(LETTERS[1:8],8,12, byrow=F), matrix(1:12,8,12, byrow=T), sep=""),8,12, dimnames = list(LETTERS[1:8], 1:12))
P96_4 <- matrix(paste(rep(4,96), matrix(LETTERS[1:8],8,12, byrow=F), matrix(1:12,8,12, byrow=T), sep=""),8,12, dimnames = list(LETTERS[1:8], 1:12))
P192_1 <- matrix(rbind(P96_1, P96_2),8,24)
P192_2 <- matrix(rbind(P96_3, P96_4),8,24)
P384_96 <- matrix(t(cbind(P192_1, P192_2)),16,24, dimnames = list(LETTERS[1:16], 1:24), byrow=T)
print("384 well plate")
print(P384, quote=F)
print("Map 4x 96 to 384")
print(P384_96, quote=F)

# (3) 384_8x48 Mapping Plate 
P48_1 <- matrix(paste(rep(1,96), matrix(LETTERS[1:8],8,6, byrow=F), matrix(1:6,8,6, byrow=T), sep=""),8,6, dimnames = list(LETTERS[1:8], 1:6))  
P48_2 <- matrix(paste(rep(2,96), matrix(LETTERS[1:8],8,6, byrow=F), matrix(1:6,8,6, byrow=T), sep=""),8,6, dimnames = list(LETTERS[1:8], 1:6))
P48_3 <- matrix(paste(rep(3,96), matrix(LETTERS[1:8],8,6, byrow=F), matrix(1:6,8,6, byrow=T), sep=""),8,6, dimnames = list(LETTERS[1:8], 1:6))
P48_4 <- matrix(paste(rep(4,96), matrix(LETTERS[1:8],8,6, byrow=F), matrix(1:6,8,6, byrow=T), sep=""),8,6, dimnames = list(LETTERS[1:8], 1:6))
P48_5 <- matrix(paste(rep(5,96), matrix(LETTERS[1:8],8,6, byrow=F), matrix(1:6,8,6, byrow=T), sep=""),8,6, dimnames = list(LETTERS[1:8], 1:6))  
P48_6 <- matrix(paste(rep(6,96), matrix(LETTERS[1:8],8,6, byrow=F), matrix(1:6,8,6, byrow=T), sep=""),8,6, dimnames = list(LETTERS[1:8], 1:6))
P48_7 <- matrix(paste(rep(7,96), matrix(LETTERS[1:8],8,6, byrow=F), matrix(1:6,8,6, byrow=T), sep=""),8,6, dimnames = list(LETTERS[1:8], 1:6))
P48_8 <- matrix(paste(rep(8,96), matrix(LETTERS[1:8],8,6, byrow=F), matrix(1:6,8,6, byrow=T), sep=""),8,6, dimnames = list(LETTERS[1:8], 1:6))
P96_48_1 <- matrix(cbind(P48_1, P48_2),8,12)
P96_48_2 <- matrix(cbind(P48_3, P48_4),8,12)
P96_48_3 <- matrix(cbind(P48_5, P48_6),8,12)
P96_48_4 <- matrix(cbind(P48_7, P48_8),8,12)
P192_48_1 <- matrix(rbind(P96_48_1, P96_48_2),8,24)
P192_48_2 <- matrix(rbind(P96_48_3, P96_48_4),8,24)
P384_48 <- matrix(t(cbind(P192_48_1, P192_48_2)),16,24, dimnames = list(LETTERS[1:16], 1:24), byrow=T)
print("Map 8x 48 to 384")
print(P384_48, quote=F)

# (4) 384_16x24 Mapping Plate 
for(i in 1:16) {
	assign(paste("P24_",i, sep=""), 
			matrix(paste(rep(i,24), 
			matrix(LETTERS[1:4],4,6, byrow=F), 
			matrix(1:6,4,6, byrow=T), sep=""),4,6, 
			dimnames = list(LETTERS[1:4], 1:6)))
}
for(i in seq(1, 16, by=2)) {
	assign(paste("P48_", which(seq(1, 16, by=2)==i), sep=""), 
			matrix(rbind(eval(parse(text=paste("P24_", i, sep=""))), eval(parse(text=paste("P24_", i+1, sep="")))),4,12))
}
for(i in seq(1, 8, by=2)) {
	assign(paste("P96_24_", which(seq(1, 8, by=2)==i), sep=""), 
matrix(t(cbind(eval(parse(text=paste("P48_", i, sep=""))), eval(parse(text=paste("P48_", i+1, sep=""))))),8,12, dimnames = list(LETTERS[1:8], 1:12), byrow=T))
}
print("Map 4x 24 to 96")
print(P96_24_1, quote=F)
P192_24_1 <- matrix(rbind(P96_24_1, P96_24_2),8,24)
P192_24_2 <- matrix(rbind(P96_24_3, P96_24_4),8,24)
P384_24 <- matrix(t(cbind(P192_24_1, P192_24_2)),16,24, dimnames = list(LETTERS[1:16], 1:24), byrow=T)
print("Map 16x 24 to 384 (not printed)")

# (5) Conversion table
df384_96_48_24 <- data.frame(P384=as.vector(P384), P96=as.vector(P384_96), P48=as.vector(P384_48), P24=as.vector(P384_24))
df384_96_48_24 <- data.frame(
			P384=sub('([A-Z])', '_\\1', as.character(df384_96_48_24[,1]), perl = TRUE), 
		 	P96=sub('([A-Z])', '_\\1', as.character(df384_96_48_24[,2]), perl = TRUE), 
			P48=sub('([A-Z])', '_\\1', as.character(df384_96_48_24[,3]), perl = TRUE),
			P24=sub('([A-Z])', '_\\1', as.character(df384_96_48_24[,4]), perl = TRUE))
df384_96_48_24 <- data.frame( # insert zeros to allow proper sorting
	P384=gsub("(_\\w)(\\d$)", "\\10\\2",as.character(df384_96_48_24[,1]), perl=T),
	P96=gsub("(_\\w)(\\d$)", "\\10\\2",as.character(df384_96_48_24[,2]), perl=T),
	P48=gsub("(_\\w)(\\d$)", "\\10\\2",as.character(df384_96_48_24[,3]), perl=T),
	P24=gsub("(_\\w)(\\d$)", "\\10\\2",as.character(df384_96_48_24[,4]), perl=T))
df384_96_48_24 <- df384_96_48_24[order(df384_96_48_24$P96),]
print("Beginning of conversion table")
print(df384_96_48_24[1:8,])

# (6) Clean things up
rm(list=ls(pattern='P192*|P96*|P48*|P24*'))

# (7) Generate mapping table for as many plates as you need
df384_96_48_24 <- data.frame(
		Pl384=gsub("_.*", "",as.character(df384_96_48_24[,1]), perl=T), Loc384=gsub(".*_", "",as.character(df384_96_48_24[,1]), perl=T),
		Pl96=gsub("_.*", "",as.character(df384_96_48_24[,2]), perl=T), Loc96=gsub(".*_", "",as.character(df384_96_48_24[,2]), perl=T),
		Pl48=gsub("_.*", "",as.character(df384_96_48_24[,3]), perl=T), Loc48=gsub(".*_", "",as.character(df384_96_48_24[,3]), perl=T),
		Pl24=gsub("_.*", "",as.character(df384_96_48_24[,4]), perl=T), Loc24=gsub(".*_", "",as.character(df384_96_48_24[,4]), perl=T))
many_df384_96_48_24 <- df384_96_48_24
many_df384_96_48_24[,c(1,3,5,7)] <- apply(many_df384_96_48_24[,c(1,3,5,7)], 2, as.numeric)
temp_df <- many_df384_96_48_24
plate_mapping_fct <- function(no_384_plates=32) {
	if(no_384_plates > 1) { 
		for(i in 1:(no_384_plates-1)) {
			temp_df <- data.frame(
						Pl384=as.numeric(as.vector(temp_df[,1]))+1, Loc384=temp_df[,2],
						Pl96=as.numeric(as.vector(temp_df[,3]))+4, Loc96=temp_df[,4],
						Pl48=as.numeric(as.vector(temp_df[,5]))+8, Loc48=temp_df[,6],
						Pl24=as.numeric(as.vector(temp_df[,7]))+16, Loc24=temp_df[,8])
			many_df384_96_48_24 <- rbind(many_df384_96_48_24, temp_df)
		}
	}
	row.names(many_df384_96_48_24) <- 1:length(many_df384_96_48_24[,1])
	many_df384_96_48_24
}
my_plate_mappings <- plate_mapping_fct(no_384_plates=32)
print("To generate mapping table for as many plates as you need, run plate mapping function like this (here 32 plates):")
print("plate_mapping_fct(no_384_plates=32)")
print("The example 'my_plate_mappings' contains the mappings for 32 384-well plates.")
print("my_plate_mappings[1:8,]")
print(my_plate_mappings[1:8,], quote=F)

# (8) Save mappings to files
# write.table(P384_96, file="P384_96.txt", row.names=T, col.names=NA, quote=F, sep="\t")
# write.table(P384_48, file="P384_48.txt", row.names=T, col.names=NA, quote=F, sep="\t")
# write.table(df384_96_48_24, file="df384_96_48_24.txt", row.names=T, col.names=NA, quote=F, sep="\t")
# write.table(my_plate_mappings, file="my_plate_mappings.txt", row.names=T, col.names=NA, quote=F, sep="\t")