R/YKOneSmapperFlour.R

In JinmiaoChenLab/oneSENSE: One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)

# Evan Newell 2015 Edited by Tan Yong Kee


#' Median heatplot generation
#'
#' This returns the median heatplot for each category of markers chosen.
#' If frequency heatplot is selected in the onesense GUI, then both median
#' and frequency heatplots are generated as PDF files in working directory
#'
#' @param LoaderPATH Name of the output file containing fcs files generated
#'     from FCStSNE2.R
#' @param Bins Number of bins to sort cells into corresponding heatplot
#' @param doCoords a boolean that allows for frequency heatplot generation
#' @param doFreq a boolean to allow for the frequency heatplot generation.
#'     TRUE to run, FALSE to not run.
#'
#' @return PNG files of combined oneSENSE and heatplot.
#'
#'
#' @import webshot
#' @importFrom flowCore exprs read.FCS
#' @importFrom plotly plot_ly subplot export layout
#' @importFrom gplots heatmap.2
#' @importFrom grDevices colorRampPalette dev.off pdf
#' @importFrom stats median
#' @importFrom graphics hist locator
#' @importFrom utils browseURL read.csv write.csv
#' @importFrom scatterplot3d scatterplot3d
#' @importFrom shinyFiles parseDirPath shinyDirButton shinyDirChoose
#'
#'
#' @examples
#' webshot::install_phantomjs()
#' #fcsoutpath <- system.file('extdata/fcs_Out',package='oneSENSE')
#' #remove hash symbol to run
#' #OneSmapperFlour(LoaderPATH=fcsoutpath) #remove hash symbol to run
OneSmapperFlour <- function(LoaderPATH = "fcs_Out",
                            Bins = 250,
                            doCoords = FALSE,
                            doFreq = FALSE) {
    message("Running OneSmapperFlour")
    fs <- read.flowSet(path = LoaderPATH, pattern = ".fcs$")
    FcsFileNames <- rownames(keyword(fs, "FILENAME"))
    FNumBC <- length(fs)
    FFdata <- NULL
    for (FFs in 1:FNumBC) {
        FFa <- exprs(fs[[FFs]])

        # Fixup column names
        colnames(FFa) <- fs[[FFs]]@parameters$desc
        empties <- which(is.na(colnames(FFa)) | colnames(FFa) == " ")
        colnames(FFa)[empties] <- fs[[FFs]]@parameters$name[empties]
        fs[[FFs]]@parameters$desc <- colnames(FFa)
        FFa <- cbind(FFa, rep(FFs, dim(FFa)[1]))
        colnames(FFa)[dim(FFa)[2]] <- "InFile"
        # Concatenate
        FFdata <- rbind(FFdata, FFa)
    }


    lgcl <- logicleTransform(w = 0.05, t = 16409, m = 4.5, a = 0)

    Xx1DtSNEmat <- NULL
    keeptable <- read.csv(paste(dirname(LoaderPATH),
                                "names.csv",
                                sep = .Platform$file.sep))
    for (factor in 2:(dim(keeptable)[2])) {
    # edited code
    keeprowbool <- sapply(keeptable[, factor], function(x) any(x == "Y"))
    keepnames <- keeptable[keeprowbool, 1]
    keeprows <- subset(keeptable, keeprowbool)
    data <- FFdata[, which(colnames(FFdata) %in% keeprows[, 1])]
    data <- cbind(data,
                FFdata[,
                which(colnames(FFdata) %in% colnames(keeptable[-1]))])

    data1 <- apply(data, 2, lgcl)
    message("Applying logicle transform")
    OneDtSNEname <- colnames(keeptable)[factor]
    dataX <- data1[, which(colnames(data1) %in% keeprows[, 1])]
    tSNEmat1 <- as.matrix(data[, OneDtSNEname])
    colnames(tSNEmat1) <- OneDtSNEname
    hist(tSNEmat1, 100)
    Xx1DtSNEmat <- cbind(Xx1DtSNEmat, tSNEmat1)

    # Make heatplot annotation


    tSNEbins <- cut(tSNEmat1, breaks = Bins, labels = 1:Bins)
    OneSENSEmed <- apply(dataX, 2,
                        function(x) (tapply(x, tSNEbins, FUN = median)))
    OneSENSEmed[is.na(OneSENSEmed)] <- 0
    pdfFN <- paste(dirname(LoaderPATH),
                    paste0(OneDtSNEname, "_Freq.pdf"),
                    sep = .Platform$file.sep)
    pdf(file = pdfFN, width = 14, height = 6)
    breaks = seq(0, 3, by = 0.005)

    my_palette <-
        colorRampPalette(c("blue", "white", "red"))(n = length(breaks) - 1)
    hmap <- heatmap.2(t(OneSENSEmed), col = my_palette, breaks = breaks,
                    margins = c(10, 20), Colv = FALSE, dendrogram = "row",
                    cexCol = 1, cexRow = 1, scale = "none", key = TRUE,
                    trace = "none", density.info = c("none"), keysize = 1)
    hmapclu = t(OneSENSEmed)[hmap$rowInd, hmap$colInd]
    hmapclut <- t(hmapclu)
    testcol <- seq(from = min(Xx1DtSNEmat),
                    to = (max(Xx1DtSNEmat) - (max(Xx1DtSNEmat)/Bins)),
                    by = (max(Xx1DtSNEmat)/Bins))
    if (OneDtSNEname == "input") {
        p1 <- plot_ly(z = hmapclu, y = rownames(hmapclu), x = testcol,
                    colors = my_palette,
                    type = "heatmap") %>% layout(title = paste(OneDtSNEname,
                                            "Median heatplot", sep = " "))
        p1
    } else {
        p2 <- plot_ly(z = hmapclut, x = colnames(hmapclut), y = testcol,
            colors = my_palette,
            type = "heatmap") %>% layout(title = paste(OneDtSNEname,
                "Median heatplot", sep = " "), showlegend = FALSE)
        p2
    }


    dev.off()

    }
    OneSplot <- plot_ly(data.frame(Xx1DtSNEmat),
                    x = Xx1DtSNEmat[, 1],
                    y = Xx1DtSNEmat[, 2],
                    marker = list(size = 5,
                                    color = 'rgba(0, 0, 0, .2)'
                                    ),
                    type = "scatter",
                    symbol = "circle-dot")
    suppressWarnings(combined <- subplot(OneSplot, p2, p1,
                                        nrows = 2,
                                        shareY = TRUE,
                                        shareX = TRUE))
    combined
    export(combined, file = paste(dirname(LoaderPATH),
            "groupone.png",
            sep = .Platform$file.sep))
    browseURL(paste(dirname(LoaderPATH),
                    "groupone.png",
                    sep = .Platform$file.sep))
}


## *************************************************************************##
## *************************************************************************##


#' Get parameters from FCS files
#' @param rawFCSdir FCS path
#'
#' @return mid
#' @export
#'
#' @examples
#' #remove hash to run
#' dir3 <- system.file('extdata/fcs', package = 'oneSENSE')
#' getParameters(dir3)
getParameters <- function(rawFCSdir) {
    fcsFile <- list.files(path = rawFCSdir,
                            pattern = ".fcs$", full.names = TRUE)
    fcs <- suppressWarnings(read.FCS(fcsFile[1]))
    pd <- fcs@parameters@data
    markers <- paste("<", pd$name, ">:", pd$desc, sep = "")
    markers_desc <- pd$desc
    gParam = list(markers = markers, markers_desc = markers_desc)

    if (length(markers) == 0) {
        stop("No markers found in the FCS file!")
    }
    return(gParam)
}
## **************************************************************************##
## **************************************************************************##
#' Generate Frequency Heatplot Part 1
#'
#' @param LoaderPATH Path of fcs_Out files
#'
#' @return Flow Frame data for coordinate selection
#' @export
#'
#'
#' @examples
#' dir1 <- system.file('extdata/fcs',package='oneSENSE')
#' OneSmapperFreq1(dir1) #remove hash symbol to run
OneSmapperFreq1 <- function(LoaderPATH = "fcs_Out") {
    fs <- read.flowSet(path = LoaderPATH, pattern = ".fcs$")
    FcsFileNames <- rownames(keyword(fs, "FILENAME"))
    FNumBC <- length(fs)
    FFdata <- NULL
    for (FFs in 1:FNumBC) {
        FFa <- exprs(fs[[FFs]])
        # Fixup column names
        colnames(FFa) <- fs[[FFs]]@parameters$desc
        empties <- which(is.na(colnames(FFa)) | colnames(FFa) == " ")
        colnames(FFa)[empties] <- fs[[FFs]]@parameters$name[empties]
        fs[[FFs]]@parameters$desc <- colnames(FFa)
        # Add file label
        FFa <- cbind(FFa, rep(FFs, dim(FFa)[1]))
        colnames(FFa)[dim(FFa)[2]] <- "InFile"
        # Concatenate
        FFdata <- rbind(FFdata, FFa)
    }
    return(FFdata)
}

## *************************************************************************##
## *************************************************************************##

#' Get Coordinates of median position
#'
#' @param LoaderPATH Path of fcs_out files
#' @param FFdata Flow frame data
#'
#' @return Assign global variables for access
#' @export
#'
#' @examples
#' #remove hash symbol to run
#' dir4 <- system.file('extdata/extra', package = 'oneSENSE')
#' file5 <- system.file('extdata/myFFdatas.rds', package = 'oneSENSE')
#' FFdata = readRDS(file5)
#' getCoords(dir4, FFdata)
getCoords <- function(LoaderPATH = LoaderPATH, FFdata = FFdata) {
    lgcl <- logicleTransform(w = 0.25, t = 16409, m = 4.5, a = 0)
    gckeeptable <- read.csv(paste(dirname(LoaderPATH),
                                "names.csv",
                                sep = .Platform$file.sep))
    gckeeprowbool <- apply(gckeeptable[, c(2, 3)],
                                1,
                                function(x) any(x == "Y"))
    gckeepnames <- gckeeptable[gckeeprowbool, 1]
    gckeeprows <- subset(gckeeptable, gckeeprowbool)
    gcdata <- FFdata[, which(colnames(FFdata) %in% gckeeprows[, 1])]
    gcdata <- cbind(gcdata,
                FFdata[, which(
                    colnames(FFdata) %in% colnames(gckeeptable[-1]))])
    data1 <- apply(gcdata, 2, lgcl)
    coordsVar <- list(keepnames = gckeepnames, data1 = data1)
    return(coordsVar)
}

## *************************************************************************##
## *************************************************************************##

#' Frequency Heatplot Generation Part 2
#'
#' @param LoaderPATH path of fcs_Out files
#' @param Bins Number of bins
#' @param FFdata Flow Frame data
#'
#' @return returns frequency heatplot
#' @export
#' @examples
#'
#' dir2 <-system.file('extdata/fcs_Out',package='oneSENSE')
#' file5 <- system.file('extdata/myFFdatas.rds', package = 'oneSENSE')
#' FFdata1 <- readRDS(file5)
#' OneSmapperFreq2(dir2, 250, FFdata1) #remove hash symbol to run
OneSmapperFreq2 <- function(LoaderPATH = "fcs", Bins = 250, FFdata) {
    lgcl <- logicleTransform(w = 0.05, t = 16409, m = 4.5, a = 0)
    Xx1DtSNEmat <- NULL
    keeptable <- read.csv(paste(dirname(LoaderPATH),
                                "names.csv",
                                sep = .Platform$file.sep))
    for (factor in 2:(dim(keeptable)[2])) {
    keeprowbool <- sapply(keeptable[, factor],
                            function(x) any(x == "Y"))
    keepnames <- keeptable[keeprowbool, 1]
    keeprows <- subset(keeptable, keeprowbool)
    data <- FFdata[, which(colnames(FFdata) %in% keeprows[, 1])]
    data <- cbind(data,
            FFdata[, which(colnames(FFdata) %in% colnames(keeptable[-1]))])
    data1 <- apply(data, 2, lgcl)  #logicle transform
    OneDtSNEname <- colnames(keeptable)[factor]
    keeprowbool <- sapply(keeptable[, factor],
                        function(x) any(x == "Y"))
    keepnames <- keeptable[keeprowbool, 1]
    keeprows <- subset(keeptable, keeprowbool)
    dataX <- data1[, which(colnames(data1) %in% keeprows[, 1])]
    tSNEmat1 <- as.matrix(data[, OneDtSNEname])
    colnames(tSNEmat1) <- OneDtSNEname
    hist(tSNEmat1, 100)
    Xx1DtSNEmat <- cbind(Xx1DtSNEmat, tSNEmat1)
    # Make heatplot annotation

    dataGNorm <- dataX
    tSNEbins <- cut(tSNEmat1, breaks = Bins, labels = 1:Bins)
    OneSENSEpp <- matrix(dataX, nrow = Bins, ncol = dim(dataX)[2])
    colnames(OneSENSEpp) <- colnames(dataX)
    Coords <- read.csv(paste(dirname(LoaderPATH),
                            "Coords.csv",
                            sep = .Platform$file.sep))
    for (pname in colnames(dataX)) {
        overthresh <- function(group) {
        # what is this group
        percpos <- (
            sum(group > Coords[which(Coords$X == pname),
                                2])/length(group)) * 100
        # print(percpos)
        return(percpos)
    }

    OneSENSEpp[, pname] <- tapply(dataX[, pname], tSNEbins, FUN = overthresh)
    }

    OneSENSEpp[is.na(OneSENSEpp)] <- 0


    pdfFN <- paste(dirname(LoaderPATH),
                    paste0(OneDtSNEname, "_Freq.pdf"),
                    sep = .Platform$file.sep)
    pdf(file = pdfFN, width = 14, height = 6)
    breaks = seq(0, 100, by = 0.05)
    my_palette <- colorRampPalette(c("blue", "white",
                                    "red"))(n = length(breaks) - 1)



    fhmap <- heatmap.2(t(OneSENSEpp),
                        col = my_palette,
                        breaks = breaks,
                        margins = c(10, 20),
                        Colv = FALSE,
                        dendrogram = "row",
                        cexCol = 1,
                        cexRow = 1,
                        scale = "none",
                        key = TRUE,
                        trace = "none",
                        density.info = c("none"),
                        keysize = 1)
    fhmapclu = t(OneSENSEpp)[fhmap$rowInd, fhmap$colInd]
    fhmapclut <- t(fhmapclu)
    ftestcol <- seq(from = min(Xx1DtSNEmat),
                    to = (max(Xx1DtSNEmat) - (max(Xx1DtSNEmat)/Bins)),
                    by = (max(Xx1DtSNEmat)/Bins))
    if (OneDtSNEname == "input") {
        suppressWarnings(d1 <- plot_ly(z = fhmapclu,
                                    y = rownames(fhmapclu),
                                    x = ftestcol,
                                    colors = my_palette,
                                    type = "heatmap") %>%
                        layout(title = paste(OneDtSNEname,
                                            "Frequency heatplot", sep = " ")))
        d1
    } else {
        suppressWarnings(d2 <- plot_ly(z = fhmapclut,
                                    x = colnames(fhmapclut),
                                    y = ftestcol,
                                    colors = my_palette,
                                    type = "heatmap") %>%
                        layout(title = paste(OneDtSNEname,
                                            "Frequency heatplot", sep = " ")))
        d2
    }
    dev.off()

    }
    OneSplot <- plot_ly(data.frame(Xx1DtSNEmat),
                        x = Xx1DtSNEmat[, 1],
                        y = Xx1DtSNEmat[, 2],
                        marker = list(size = 5,
                                    color = 'rgba(0, 0, 0, .2)'
                        ),
                        type = "scatter",
                        symbol = "circle-dot")
    suppressWarnings(fcombined <- subplot(OneSplot, d2, d1, nrows = 2,
                                shareY = TRUE, shareX = TRUE))
    fcombined
    export(fcombined, file = paste(dirname(LoaderPATH),
                                "grouptwo.png",
                                sep = .Platform$file.sep))

    browseURL(paste(dirname(LoaderPATH),
                "grouptwo.png",
                sep = .Platform$file.sep))

}