R/plate2df.R

In bioassays: Summarising Multi Well Plate Cellular Assay

#'@name plate2df
#'
#'@aliases plate2df
#'
#'@title Format Matrix Type 2D Data of Multi well Plate as Dataframe
#'
#'@description This function uses column names and row names of  'datamatrix' (2D data of a mutli well plate) and generate a dataframe with row, col (column) and position indices. The 'value' column represent corresponding value in the 'datamarix'.
#'
#'@usage plate2df(datamatrix)
#'
#'@param datamatrix datamatrix is the 2D data of a mutli well plate. Usually the result of \code{\link{data2plateformat}}:
#'
#'@return A dataframe with 4 columns. Number of rows is equal to the number of wells (plate type of 'datamatrix'). The columns represent
#'\item{row }{Row number of the entry}
#'\item{col }{Column number of the entry}
#'\item{position }{Position (Row+column number) of the entry}
#'\item{value}{Individual entries in the 'datamatrix'}
#'
#'
#'@author A.A Palakkan
#'
#'@examples
#'## loading data
#'data(rawdata24,rawdata96,rawdata384)
#'
#'## eg:1 spectrophotometer reading from 24 well plate in dataframe format
#'datamatrix<- data2plateformat(rawdata24, platetype = 24)
#'head(plate2df(datamatrix))
#'
#'## eg:2 spectrophotometer reading from 96 well plate in dataframe format
#'datamatrix<- data2plateformat(rawdata96, platetype = 96)
#'head(plate2df(datamatrix))
#'
#'## eg:3 spectrophotometer reading from 384 well plate in dataframe format
#'datamatrix<- data2plateformat(rawdata384, platetype = 384)
#'head(plate2df(datamatrix))
#'
#'@keywords manip
#'
#' @export
#'

plate2df<- function (datamatrix){

position <- value <- NULL
platelayout <- data.frame(row = rep(rownames(datamatrix),length(colnames(datamatrix)))
                             , col = rep(colnames(datamatrix),each =length(rownames(datamatrix))))

platelayout$col<-formatC(platelayout$col, width = 2,flag = 0)
platelayout$position <- paste0(platelayout$row,sprintf("%02d", as.numeric(platelayout$col)))

#platelayout$position <- paste0(platelayout$row, platelayout$col)
#platelayout$position <- sub("^(.)(.)$", "\\10\\2", platelayout$position, perl=T)
platelayout <- platelayout[order(platelayout$position),]
rownames(platelayout)<-c(seq_along(rownames(platelayout)))

platelayout$value<-0
for(i in seq_along(rownames(platelayout)))
{platelayout[i,4]<-datamatrix[as.character(platelayout[i,]$row),as.numeric(platelayout[i,]$col)]}


platelayout <- transform(
                  platelayout,
                  row=as.character(row),
                  col=as.integer(col),
                  position=as.character(position),
                  value=as.numeric(value))

return(platelayout)
}