plotPCA: PCA Plot for Device
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Author(s) See Also

This function produces a PCA plot of the first two principle components for the selected device.

plotPCA(x,
        which      = "UnitName",
        transfo    = log2,
        method     = "none",
        groups     = NULL,
        screeplot  = FALSE,
        squarepca  = FALSE,
        pcs        = c(1,2),
        add.labels = FALSE,
        add.legend = FALSE,
        col        = NULL,
        names      = "namepart",
        as.list    = FALSE,
        dev        = "screen",
        outfile    = "PCAPlot",
        w          = 540,
        h          = 540,
        ...)

`x`	object of class `ExprTreeSet`.
`which`	type of probes to be used, for details see `validData`.
`transfo`	a valid function to transform the data, usually “log2”, or “0”.
`method`	a character string indicating which correlation coefficient is to be computed. One of “pearson”, “spearman”, “kendall”, or “none”.
`groups`	character `vector` listing the group names in order of the `names`.
`screeplot`	logical, if TRUE plot a `screeplot` instead of a PCA plot.
`squarepca`	logical, if TRUE make the y-axis of the PCA plot comparable to the x-axis.
`pcs`	a character `vector` of length two indicating which principal components to plot.
`add.labels`	logical, if TRUE then name labels will be added to the points.
`add.legend`	logical, if TRUE and `groups` are supplied then a legend indicating the groups will be drawn. Optionally, a character indicating the position of the legend, default is “topleft”.
`col`	vector of colors for plot, length is number of samples.
`names`	optional vector of sample names.
`as.list`	logical, if TRUE then a `list` will be returned in addition to the plot.
`dev`	graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.
`outfile`	the name of the output file.
`w`	the width of the device in pixels.
`h`	the height of the device in pixels.
`...`	optional arguments to be passed to `plot`.

Function plotPCA produces a PCA plot of the first two principle components for slot data or the correlations between the columns of slot data, respectively, of an object of class ExprTreeSet.

For method="none" function [stats]prcomp will be applied to slot data directly, otherwise prcomp will be applied to (1 - cor(data)) with the respective method.

For screeplot=TRUE a screeplot will be plotted instead of a PCA plot.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as mvaplot.

Christian Stratowa

pcaplot

xps documentation built on Nov. 8, 2020, 6 p.m.