# densityplot: Function to make density plots In machalen/QualityGraphs: Make quality graphs for microarray data based on objects obtained witharoma affymetrix normalization.

## Usage

 `1` ```densityplot(ds, strt = NULL, nd = NULL, lab, parameters) ```

## Arguments

 `ds` `strt` `nd` `lab` `parameters`

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47``` ```##---- 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, lab, parameters) { 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) } yvalues <- vector() for (o in strt:nd) { fitxer <- getFile(ds, idx = o) dl <- log(aroma.affymetrix::getData(fitxer, fields = "intensities", indices = 1:nbrOfCells(fitxer))\$intensities, base = 2) ycoor <- ceiling(max(density(dl)\$y)) yvalues <- c(yvalues, ycoor) } colors <- rainbow(nd - strt + 1) fitxer <- getFile(ds, idx = strt) dl <- log(aroma.affymetrix::getData(fitxer, fields = "intensities", indices = 1:nbrOfCells(fitxer))\$intensities, base = 2) plot(density(dl), col = colors[1], main = paste("Samples", strt, "to", nd), xlab = "log2(y)", ylim = c(0, max(yvalues)), lty = strt, ylab = "") for (e in (strt + 1):nd) { fitxer <- getFile(ds, idx = e) dl <- log(aroma.affymetrix::getData(fitxer, fields = "intensities", indices = 1:nbrOfCells(fitxer))\$intensities, base = 2) lines(density(dl), col = colors[(e - strt) + 1], lty = e) } if (length(lab) < 15) { legend("topright", legend = lab, cex = 0.6, col = colors[1:nd], lty = strt:nd, lwd = 1.6) } else { legend("topright", legend = lab, cex = parameters\$ce, col = colors[1:nd], lty = strt:nd, lwd = 1.6) } } ```

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