rnb.plot.dreduction: rnb.plot.dreduction

Description

Creates a dimension reduction plot based on the methylation values of the given dataset.

Usage

rnb.plot.dreduction(rnb.set, plot.type = "pca", dimensions = 1:2, distance.metric = "euclidean", target = "sites", point.types = 0L, point.colors = 0L, legend.space = 2)

Arguments

rnb.set

Methylation dataset as an object of type inheriting RnBSet. This dataset must contain at least four samples.

plot.type

Type of plot to be created. This must be one of "pca" (projection to two principal components) or "mds" (multidimensional scaling to two dimensions). The section Details provides more details on how the dimension reduction techniques are applied.

dimensions

Vector of two positive integer values giving the principle components to be shown in the horizontal and vertical axis of the plot. This parameter is considered only when plot.type is "pca".

distance.metric

Distance metric to be applied when reducing the dimensionality of the methylation data. This must be one of "eucledian" or "manhattan". The second metric is supported only in multidimensional scaling.

target

Site or region type to be used in the dimension reduction technique. This must be either "sites" (individual CpGs) or one of the region types summarized in rnb.set.

point.types

Trait, specified as column name or index in the sample annnotation table of rnb.set, to be used to define point types in the plot. Setting this parameter to zero (default) or to a trait that does not define categories results in all samples being displayed as filled circles. If this parameter specifies a column that can be used as sample identifiers, the plot displays the samples as identifiers instead of points.

point.colors

Trait, specified as column name or index in the sample annnotation table of rnb.set, to be used to define sample colors in the plot. Setting this parameter to zero (default) or to a trait that does not define categories results in all samples being displayed in black.

legend.space

Width, in inches, of the space dedicated for legends that will be assigned on the right side of the plot. This parameter is considered only if legends are actually included, that is, if sample traits are mapped to point types and/or colors.

Value

The generated plot as an object of type ggplot. The object also contains an attribute "info", which is a list with the following elements:

"Target": Targeted sites or regions; the value of the parameter target.
"Technique": Dimension reduction technique applied; one of "PCA" or "MDS".
"All": Total number of sites or regions defining the high dimensional methylation space.
"Missing": Number of dimensions ignored because they contain (only) missing values.
"Selected": Number of dimensions used when applying a dimension reduction technique.
"Explained": Value between 0 and 1 showing the variance explained by the selected dimensions, as a fraction of the total variance of all dimensions.

Details

The analysis option "exploratory.top.dimensions" controls whether dimension reduction is applied on all probes, sites or regions available in the given dataset, or only on the most variable ones. In case a trait is mapped to point types, the shapes to use are taken from the option "points.category". Similary, the option "colors.category" determines which colors are used when mapping to color is applied. See RnBeads Options for more information on these options.

Examples

Run this code


library(RnBeads.hg19)
data(small.example.object)
pdf("PCA.pdf", width = 7.2, height = 5.2)
print(rnb.plot.dreduction(rnb.set.example, point.colors="Sample_Group"))
dev.off()