R/plate96.R

In wolass/rlabbook: Package for electronic (wet) lab notebook keeping

# this function makes a matrix with colnames and rownames well prepared for the experiments with 96 well plates
# this function is taking either vector of length 96 or a matrix
# it returns a matrix with colnames and rownames and prints it in the landscape or vertical forms what depends on the 'landscape' variable.
#' @export

plate96 <- function(ts,times,folder,file,sam.dat){
    dbs <- lapply(paste0(folder,ts,".pdf"),extract.revelation)
    df<- data.frame(dbs)
    data <- tidyr::gather(df,key = "T1",value = "OD")
    data$OD <- as.numeric(data$OD)
    data$time <- unlist(lapply(times,rep,96))
    data$time <- as.POSIXct(data$time,format="%H:%M")
    data$time <- (data$time - data$time[1])/3600
    data$time <- as.numeric(data$time)
    # data$time[(96*7+1):length(data$time)] <- data$time[(96*7+1):length(data$time)]+(60*60*24)
    data$sample <-rep(sapply(1:12,paste0,LETTERS[1:8]),length(dbs))
    data$row <- rep(LETTERS[1:8],length(dbs))
    data$column <- rep(sapply(1:12,rep,8),length(dbs))
    save(data,file = paste0(folder,file))
    return(data)
}



# plate96 <- function(x,landscape=TRUE){
#     if(landscape==TRUE){
#         m.ncol=12
#         if(is.vector(x)==TRUE&length(x)==96){ #check if a vector or a matric was given
#             plate<-matrix(x,ncol=m.ncol)
#             colnames(plate)<- as.character(c(1:12))
#             rownames(plate) <- LETTERS[1:8]
#         }else if(is.matrix(x)==TRUE&length(x)==96){
#             plate<-x
#             colnames(plate)<- as.character(c(1:12))
#             rownames(plate) <- LETTERS[1:8]
#         }else{
#             stop("Not a vector of length 96 nor a matrix")
#         }
#     }else{
#         m.ncol=8
#         if(is.vector(x)==TRUE&length(x)==96){ #check if a vector or a matric was given
#             plate<-matrix(x,ncol=m.ncol)
#             rownames(plate)<- as.character(c(1:12))
#             colnames(plate) <- LETTERS[1:8]
#         }else if(is.matrix(x)==T&length(x)==96){
#             if(ncol(x)==12){
#                 plate <- t(x)
#                 rownames(plate)<- as.character(c(1:12))
#                 colnames(plate) <- LETTERS[1:8]
#             }else if(ncol(x)==8){
#                 plate <- x
#                 rownames(plate)<- as.character(c(1:12))
#                 colnames(plate) <- LETTERS[1:8]
#             }else{
#                 stop("Matrix not conformant with the plate size. make it either 8 or 12 colums/rows")
#             }
#
#         }
#     }
#     return(plate)
#
# }