You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
67 lines
2.8 KiB
R
67 lines
2.8 KiB
R
#' Create sampleid from path to experiment datafile
|
|
#'
|
|
#' Returns a "unique" sample ID when supplied with a path to an experimental file.
|
|
#' The second arg is optional, defaults to "old" behaviour,
|
|
#' but can be set to "dirname" for another behaviour.
|
|
#' The second arg was added so as not to break older code.
|
|
#'
|
|
#' @param pathexpfile path to an experiment datafile
|
|
#' @param implementation defaults to "old" behaviour, can also be set to "dirname"
|
|
#'
|
|
#' @return a sampleid (character string)
|
|
#' @export
|
|
ProvideSampleId <- function (pathexpfile, implementation = "filename") {
|
|
## Note to myself: the sample ID must derive directly from the file or path.
|
|
if (implementation == "dirname") {
|
|
# basename(dirname()) returns the name of the lowest sub-directory
|
|
# split()[[1]][2] splits the dirname at the hyphen and returns the sampleid
|
|
sampleid <- strsplit(x = basename(dirname(pathexpfile)),
|
|
split = "-")[[1]][2]
|
|
} else {
|
|
# basename() returns the filename sans path
|
|
# sub() returns the filename sans extension
|
|
sampleid <- sub("\\.[\\w]+$", "", basename(pathexpfile), perl = TRUE)
|
|
}
|
|
|
|
return(sampleid)
|
|
}
|
|
|
|
|
|
#' Display the history of a substrate (sampleid)
|
|
#'
|
|
#' @param sampleid string
|
|
#' @param matrix.rda path to rdata file containing the sample matrix
|
|
#'
|
|
#' @return a dataframe
|
|
#' @export
|
|
SubstrateHistory <- function(sampleid, matrix.rda) {
|
|
matrix <- LoadRData2Variable(matrix.rda)
|
|
# Extract the rows pertaining to the current sampleid
|
|
sample.history <- matrix[which(matrix$sampleid == sampleid), ]
|
|
# Loops remove all "\\labreport{...}" strings (they make the table too wide otherwise)
|
|
for (j in 1:dim(sample.history)[1]) {
|
|
for (k in 1:dim(sample.history)[2]) {
|
|
sample.history[j, k] <- gsub("^\\\\labreport.*?\\}\\{", "", sample.history[j, k])
|
|
sample.history[j, k] <- gsub("\\}$", "", sample.history[j, k])
|
|
}
|
|
}
|
|
# Find empty columns and collect their column indices
|
|
empty.cols <- matrix(data = FALSE, nrow = 1, ncol = dim(sample.history)[2])
|
|
for (k in 1:dim(sample.history)[2]) {
|
|
if (paste(sample.history[, k], collapse = "") == "") {
|
|
empty.cols[, k] <- TRUE
|
|
}
|
|
}
|
|
# Save the names of the empty columns
|
|
empty.names <- names(sample.history)[which(empty.cols)]
|
|
# Remove the identified empty columns plus those columns deemed unwanted
|
|
sample.history <- sample.history[, -c(which(empty.cols == TRUE),
|
|
#which(names(sample.history) == "sampleid"),
|
|
which(names(sample.history) == "created"),
|
|
which(names(sample.history) == "project"))]
|
|
# Save the empty column names as attribute to sample.history dataframe
|
|
attr(sample.history, "empty.names") <- empty.names
|
|
|
|
return(sample.history)
|
|
}
|