#' convenient reporting of sample name and design
#'
#' @details convenience function reporting of sample names. writes text file with sample summary.
#' @param ramclustObj ramclustR object summarize
#' @param which.data character; which dataset (SpecAbund or SpecAbundAve) to perform PCA on.
#' @param delim character; "-" by default - the delimiter for parsing sample names to factors
#' @param cmpdlabel = "cmpd"; label the data with the annotation. can also be set to 'ann' for column names assigned as annotatins.
#' @return returns a ramclustR Object, with sample summary appended to 'sampleSummary'slot.
#' @concept RAMClustR
#' @author Corey Broeckling
#' @export
reportSampleNames<-function(
ramclustObj=NULL,
which.data="SpecAbund",
delim="-",
cmpdlabel="cmpd",
filename = NULL
) {
if(is.null(filename)) {
if(!dir.exists("tmp.report")) {dir.create("tmp.report")}
filename <- "tmp.report/sample.names.txt"
}
d <- getData(ramclustObj = ramclustObj, which.data = which.data, delim = delim, cmpdlabel = cmpdlabel)
out <- paste("The sample set after all processing contains", nrow(ramclustObj[[which.data]]), "samples analyses.", '\n')
out <- paste0(out, "Factors are summarized as 'Factor Name' - 'factor level' : 'number of reps'", '\n')
for(i in 1:ncol(d[[1]])) {
tmp <- table(d[[1]][,i])
if(max(tmp) < 2) {next}
out <- paste(out, " ", names(d[[1]])[i], " ",
paste(names(tmp), tmp, collapse = '; ', sep = ":"),
'\n'
)
}
ramclustObj$sampleSummary <- out
sink(filename)
cat(out)
sink()
# cat(out)
cat(paste0("File written to ", getwd(), "/", filename, '\n'))
return(ramclustObj)
}
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