boxplot_raw: Boxplots for raw data in log2 scale

In machalen/QualityGraphs: Make quality graphs for microarray data based on objects obtained witharoma affymetrix normalization.

Usage

boxplot_raw(ds, strt = NULL, nd = NULL, parameters, lab, conditions = NULL, colors = NULL)

Arguments

ds
strt
nd
parameters
lab
conditions
colors

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (ds, strt = NULL, nd = NULL, parameters, lab, conditions = NULL, 
    colors = NULL) 
{
    if (is.null(labels)) {
        labels <- gsub(paste("_(", xip, ")", sep = ""), "", ds$Names, 
            fixed = TRUE)
    }
    if (is.null(strt) & is.null(nd)) {
        strt <- 1
        nd <- length(ds)
    }
    else if (is.null(strt)) {
        strt <- 1
    }
    else if (is.null(nd)) {
        nd <- length(ds)
    }
    fitxer_int <- as.list(1:nd)
    for (i in (strt:nd)) {
        fitxer <- getFile(ds, idx = i)
        fitxer_int[[i]] <- log(aroma.affymetrix::getData(fitxer, 
            fields = "intensities", indices = 1:nbrOfCells(fitxer))$intensities, 
            base = 2)
    }
    if (is.null(conditions)) {
        boxplot(fitxer_int[strt:nd], main = "Boxplot rawdata ", 
            xaxt = "n")
        axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
            las = 2)
    }
    else if (is.null(colors)) {
        CondNames <- mixedsort(lab)
        CondTable <- data.frame(CondNames, conditions)
        conditions.o <- CondTable[match(lab, CondTable$CondNames), 
            "conditions"]
        list1 <- unique(as.character(sort(conditions.o)))
        ColVect <- c(brewer.pal(8, "Dark2"), brewer.pal(12, "Paired"))
        list2 <- ColVect[1:length(unique(conditions.o))]
        map = setNames(list2, list1)
        colors <- map[conditions.o]
        boxplot(fitxer_int[strt:nd], main = "Boxplot rawdata ", 
            xaxt = "n", col = colors)
        axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
            las = 2)
        legend("topright", legend = list1, cex = 0.5, fill = list2)
    }
    else {
        CondNames <- mixedsort(lab)
        CondTable <- data.frame(CondNames, conditions)
        conditions.o <- CondTable[match(lab, CondTable$CondNames), 
            "conditions"]
        list1 <- unique(as.character(sort(conditions.o)))
        list2 <- colors
        map = setNames(list2, list1)
        colors <- map[conditions.o]
        boxplot(fitxer_int[strt:nd], main = "Boxplot rawdata ", 
            xaxt = "n", col = colors)
        axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
            las = 2)
        legend("topright", legend = list1, cex = 0.5, fill = list2)
    }
  }

machalen/QualityGraphs documentation built on Oct. 22, 2019, 8:29 p.m.