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#' Create sampleid from path to experiment datafile
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#'
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#' Returns a "unique" sample ID when supplied with a path to an experimental file.
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#' The second arg is optional, defaults to "old" behaviour,
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#' but can be set to "dirname" for another behaviour.
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#' The second arg was added so as not to break older code.
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#'
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#' @param pathexpfile path to an experiment datafile
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#' @param implementation defaults to "old" behaviour, can also be set to "dirname"
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#'
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#' @return a sampleid (character string)
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#' @export
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ProvideSampleId <- function (pathexpfile, implementation = "filename") {
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## Note to myself: the sample ID must derive directly from the file or path.
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if (implementation == "dirname") {
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# basename(dirname()) returns the name of the lowest sub-directory
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# split()[[1]][2] splits the dirname at the hyphen and returns the sampleid
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sampleid <- strsplit(x = basename(dirname(pathexpfile)),
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split = "-")[[1]][2]
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} else {
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# basename() returns the filename sans path
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# sub() returns the filename sans extension
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sampleid <- sub("\\.[\\w]+$", "", basename(pathexpfile), perl = TRUE)
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}
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return(sampleid)
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}
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#' Extract sampleid from a string
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#'
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#' Extract sampleid from a string by utilising the fact that samepleid's
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#' adhere to a defined format.
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#'
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#' @param string character string that contains a sampleid
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#'
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#' @return sampleid (character string)
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#' @export
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ExtractSampleIdString <- function(string) {
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# regmatches() extracts matched substrings based on the results of regexpr and friends
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# another way to do this would be stringr::str_extract()
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sampleid <-
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regmatches(string, regexpr("\\d{1,2}[A-Za-z]{1}\\d{2,4}", string))
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# return empty string rather than character(0)
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if (length(sampleid) == 0) sampleid <- ""
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return(sampleid)
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}
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#' Display the history of a substrate (sampleid)
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#'
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#' @param sampleid string
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#' @param matrix.rda path to rdata file containing the sample matrix
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#'
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#' @return a dataframe
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#' @export
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SubstrateHistory <- function(sampleid, matrix.rda) {
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matrix <- LoadRData2Variable(matrix.rda)
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# Extract the rows pertaining to the current sampleid
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sample.history <- matrix[which(matrix$sampleid == sampleid), ]
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# Loops remove all "\\labreport{...}" strings (they make the table too wide otherwise)
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for (j in 1:dim(sample.history)[1]) {
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for (k in 1:dim(sample.history)[2]) {
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sample.history[j, k] <- gsub("^\\\\labreport.*?\\}\\{", "", sample.history[j, k])
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sample.history[j, k] <- gsub("\\}$", "", sample.history[j, k])
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}
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}
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# Find empty columns and collect their column indices
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empty.cols <- matrix(data = FALSE, nrow = 1, ncol = dim(sample.history)[2])
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for (k in 1:dim(sample.history)[2]) {
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if (paste(sample.history[, k], collapse = "") == "") {
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empty.cols[, k] <- TRUE
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}
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}
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# Save the names of the empty columns
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empty.names <- names(sample.history)[which(empty.cols)]
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# Remove the identified empty columns plus those columns deemed unwanted
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sample.history <- sample.history[, -c(which(empty.cols == TRUE),
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#which(names(sample.history) == "sampleid"),
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which(names(sample.history) == "created"),
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which(names(sample.history) == "project"))]
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# Save the empty column names as attribute to sample.history dataframe
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attr(sample.history, "empty.names") <- empty.names
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return(sample.history)
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}
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