biosvd (version 2.8.0)

EigensystemPlotParam-class: The EigensystemPlotParam class

Description

EigensystemPlotParam is a list-based class for storing the parameters needed to specify plot features used by link{plot,plot-method} in plotting Eigensystem diagnostics, projections and transformations.

Slots

EigensystemPlotParam objects contain the following slots

plots:

character vector indicating one or more plot choices from: "eigenfeatureHeatmap", "eigenassayHeatmap", "sortedHeatmap", "fraction","scree","zoomedFraction", "lines", "allLines", "eigenfeaturePolar", "eigenassayPolar". Defaults to all.

palette:

function defining the palette to be used for heatmaps. Default is a Blue-Yellow color ramp.

whichAssays:

numeric vector listing which assays are to be included in the plot(s). Default is all.

whichFeatures:

numeric vector which features to include in plots. Default is all.

whichEigenassays:

numeric vector which eigenassays to include in plots.

whichEigenfeatures:

numeric vector which eigenfeatures to include in plots. Defaults to first four.

whichPolarAxes:

numeric vector which two eigenassays/eigenfeatures to include in polar plots. Default is first two.

assayColorMap:

assayColorMap and featureColorMap are optional lists of colors corresponding to the levels of these annotations for assays and features. The elements of each list are named by the annotation column they correspond to. Each element is itself a named vector of colors, named by the level of the annotation it reflects (see example).

featureColorMap:

list

contrast:

numeric value specifying the contrast to use in heatmaps.

negativeValues:

logical indicating whether scaling of values for heatmap should result in range that includes negative values. Default is TRUE.

path:

character specifying the path of files for figure output. Default is current working directory.

prefix:

character specifying an optional prefix to add to filenames. Default is biosvd.

filenames:

character optional name for the files containing the plots. Names correspond to elements of 'plots' vector.

figure:

logical specifying whether to ouptut plots into files. Default is FALSE.

Accessors

plots(x), plots(x) <- value

palette(x), palette(x) <- value

whichAssays(x), whichAssays(x) <- value

whichFeatures(x), whichFeatures(x) <- value

whichEigenassays(x), whichEigenassays(x) <- value

whichEigenfeatures(x), whichEigenfeatures(x) <- value

whichPolarAxes(x), whichPolarAxes(x) <- value

assayColorMap(x), assayColorMap(x) <- value

featureColorMap(x), featureColorMap(x) <- value

contrast(x), contrast(x) <- value

negativeValues(x), negativeValues(x) <- value

path(x), path(x) <- value

prefix(x), prefix(x) <- value

filenames(x), filenames(x) <- value

figure(x), figure(x) <- value

Details

The EigensystemPlotParam class stores the list of desired plots, color palettes and keys, figure file and directory names and other necessary parameters. Data in the EigensystemPlotParam may be organized into slots: ‘plots’, ‘palette’, ‘whichAssays’, ‘whichFeatures’, ‘whichEigenassays’, ‘whichEigenfeatures’, ‘whichPolarAxes’, ‘assayColorMap’, ‘featureColorMap’, ‘contrast’, ‘negativeValues’, ‘path’, ‘prefix’, ‘filename’, ‘figure’, brief descriptions of which follow.

References

Alter O, Brown PO and Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U.S.A. 97(18), 10101-10106 (2000).

Examples

data(YeastData_alpha)

params <- new("EigensystemPlotParam")
cellcycle.col.map <- c("orange2", "darkgreen", "blue2", "magenta2", "red2")
names(cellcycle.col.map) <- c("S", "G2", "M", "M/G1", "G1")
assayColorMap(params) <- list(Cell.cycle.stage=cellcycle.col.map)
featureColorMap(params) <- list(Cell.cycle.stage=NA)