RLE_NUSE_oligo: Function to make NUSE and RLE boxplots.

In machalen/QualityGraphsOligo: Make quality graphs for microarray data based on objects obtained with oligo normalization.

Usage

RLE_NUSE_oligo(Pset, kind, parameters, lab, conditions = NULL, colors = NULL)

Arguments

Pset
kind
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 (Pset, kind, parameters, lab, conditions = NULL, colors = NULL) 
{
    if (kind == "NUSE") {
        if (is.null(conditions)) {
            oligo::NUSE(Pset, main = paste(kind, "plot"), 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))]
            map = setNames(list2, list1)
            colors <- map[conditions.o]
            oligo::NUSE(Pset, main = paste(kind, "plot"), xaxt = "n", 
                col = colors)
            axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
                las = 2)
            legend("topright", legend = list1, cex = parameters$ce + 
                0.2, fill = list2)
        }
        else {
            CondNames <- mixedsort(lab)
            CondTable <- data.frame(CondNames, conditions)
            conditions.o <- CondTable[match(lab, CondTable$CondNames), 
                "conditions"]
            list1 <- unique(as.character(sort(conditions.o)))
            list2 <- colors
            map = setNames(list2, list1)
            colors <- map[conditions.o]
            oligo::NUSE(Pset, main = paste(kind, "plot"), xaxt = "n", 
                col = colors)
            axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
                las = 2)
            legend("topright", legend = list1, cex = parameters$ce + 
                0.2, fill = list2)
        }
    }
    else if (kind == "RLE") {
        if (is.null(conditions)) {
            oligo::RLE(Pset, main = paste(kind, "plot"), xaxt = "n")
            axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
                las = 2)
        }
        else if (is.null(colors)) {
            CondNames <- mixedsort(lab)
            CondTable <- data.frame(CondNames, conditions)
            conditions.o <- CondTable[match(lab, CondTable$CondNames), 
                "conditions"]
            list1 <- unique(as.character(sort(conditions.o)))
            ColVect <- c(brewer.pal(8, "Dark2"), brewer.pal(12, 
                "Paired"))
            list2 <- ColVect[1:length(unique(conditions))]
            map = setNames(list2, list1)
            colors <- map[conditions.o]
            oligo::RLE(Pset, main = paste(kind, "plot"), xaxt = "n", 
                col = colors)
            axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
                las = 2)
            legend("topright", legend = list1, cex = parameters$ce + 
                0.2, fill = list2)
        }
        else {
            CondNames <- mixedsort(lab)
            CondTable <- data.frame(CondNames, conditions)
            conditions.o <- CondTable[match(lab, CondTable$CondNames), 
                "conditions"]
            list1 <- unique(as.character(sort(conditions.o)))
            list2 <- colors
            map = setNames(list2, list1)
            colors <- map[conditions.o]
            oligo::RLE(Pset, main = paste(kind, "plot"), xaxt = "n", 
                col = colors)
            axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
                las = 2)
            legend("topright", legend = list1, cex = parameters$ce + 
                0.2, fill = list2)
        }
    }
  }

machalen/QualityGraphsOligo documentation built on May 28, 2019, 2:32 a.m.