R/cl_classFunctions.R

In bpollner/flowdex: Extract Fluorescence Distribution Data from FCS Files and Recalculate to Events per Volume

#### regarding gating set ####

show_GatingSet_flowWorkspace <- function(object) {
    saNames <- flowWorkspace::sampleNames(object)
    nr <- seq_along(saNames)
    isnDF <- data.frame(nr, saNames)
    colnames(isnDF) <- c("Index", "SampleNames")
    #
    colNames <- flowWorkspace::colnames(object)
    #
    txtA <- paste0("A GatingSet of class 'GatingSet' with ", length(saNames), " samples:\n\n")
    txtB <- paste0("The following ", length(colNames), " channels are available:\n", paste(colNames, collapse="    "))
    #
    cat(txtA)
    print(isnDF)
    cat("\n\n")
    cat(txtB)
    #
    return(invisible(NULL))
} # EOF

show_GatingSet_fd <- function(object) {
    saNames <- flowWorkspace::sampleNames(object)
    nr <- seq_along(saNames)
    isnDF <- data.frame(nr, saNames)
    colnames(isnDF) <- c("Index", "SampleNames")
    #
    colNames <- flowWorkspace::colnames(object)
    #
    txtA <- paste0("A GatingSet of class 'GatingSet_fd' with ", length(saNames), " samples:\n\n")
    txtB <- paste0("The following ", length(colNames), " channels are available:\n", paste(colNames, collapse="    "))
    txtC <- paste0("The following gating strategy derived from file '", object@gateStrat@filename, "' has been applied:\n")
    #
    cat(txtA)
    print(isnDF)
    cat("\n\n")
    cat(txtB)
    cat("\n\n")
    cat(txtC)
    print(object@gateStrat)
    #
    return(invisible(NULL))
} # EOF

show_fdmat <- function(object) {
    #
    txtGaAdd <- ""
    #
    reToVol <- all(unlist(lapply(object, function(x) nrow(x@eventsPerVol)))) > 0
    if (reToVol) {
        volUnit <- object[[1]]@eventsPerVol@volumeUnit
        volTxt <- paste0("Fluorescence distribution has been re-calculated to events per ", volUnit, ".\n")
    } else {
        volTxt <- "Fluorescence distribution has *NOT* been re-calculated to events per volume unit.\n"
    } # end else
    
    
    nrSamples <- nrow(object@pData)
    nrGates <- nrow(object@metadata)
    if (nrGates > 1) {txtGaAdd <- "s"}
    txt0 <- "An object of class 'fdmat' [package 'flowdex'] with 6 slots\n"
    txt1 <- paste0("containing data from ", nrSamples, " samples in ", nrGates, " gate", txtGaAdd, ".\n") 
    txt2 <- paste0("(use 'object[[1]]' to inspect the first list element containing the first fluorescence distribution)\n")
    #
    cat(txt0)
    cat(txt1)
    cat(volTxt)
    cat(txt2)
#    matShow <- object@.Data[c(1,2,nr-1, nr), c(1:3, nc-2, nc-1, nc)]
#    print(matShow)
#    cat(txt2)
    #
    cat("\n\nSlot 'metadata':\n")
    print(object@metadata)

    cat("\n\nSlot 'cyTags':\n")
    print(object@cyTags)

#    cat("\n\nSlot 'eventsPerVol':\n")
#    print(object@eventsPerVol)
    
    cat("\n\nSlot 'gateStrat':\n")
    print(object@gateStrat)
    
    cat("\n\nSlot 'pData':\n")
    print(object@pData)
    
    cat("\n\nSlot 'note':\n")
    print(object@note)
    #
    return(invisible(NULL))
} # EOF

show_fdmat_single <- function(object) {

    nC <- ncol(object)
    nSa <- nrow(object)
    cns <- colnames(object)
    from <- cns[1]
    to <- cns[length(cns)]
    #
    txt0 <- "An object of class 'fdmat_single'\n"
    txt1 <- paste0("containing data from ", nSa, " samples in ", nC, " fluorescence intensities from ", from, " to ", to, "\n")
    txt11 <- paste0("derived from gate '", object@gateName, "'.\n")
    txt2 <- "(showing only the first and last columns and rows)\n"
    txtOveralEVPV <- "Overall data for events per volume unit:\n"
    txtNote <- paste0(object@note, " \n")
    if (nrow(object) < 5) {
        matShow <- object[, c(1,2,3, nC-2, nC-1,nC)] 
    } else {
        matShow <- object[c(1,2, nSa-1, nSa), c(1,2,3, nC-2, nC-1,nC)]
    }
    cat(txt0)
    cat(txt1)
    cat(txt11)
    cat(txtNote)    
    print(matShow)
    cat(txt2)
    cat("\n")
    cat(txtOveralEVPV)
    print(object@eventsPerVol)    
    return(invisible(NULL))
} # EOF