plot.jive: Create Plots for a JIVE Object

Description Usage Arguments Author(s) References See Also Examples

View source: R/jive.r

Description

Three types of plots are available. By default (or type="var"), this creates a bar plot showing the percentage of variability attributable to joint structure, individual structure, and residual variance. With type="heat", it will create a series of heatmaps. With type="pca", it will give principal component plots.

Usage

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## S3 method for class 'jive'
plot(x, type="var", ...)

Arguments

x

An object of class "jive" to be plotted.

type

A string indicating the type of plot. The default, "var", generates a bar plot of the variance explained, "heat" generates a heatmap, and "pca" generates principal component plots.

...

Additional arguments to pass to the specific plotting functions. See documentation for showVarExplained,showHeatmaps, and showPCA for more details.

Author(s)

Michael J. O'Connell and Eric F. Lock

References

Lock, E. F., Hoadley, K. A., Marron, J. S., & Nobel, A. B. (2013). Joint and individual variation explained (JIVE) for integrated analysis of multiple data types. The Annals of Applied Statistics, 7(1), 523-542.

O'Connell, M. J., & Lock, E.F. (2016). R.JIVE for Exploration of Multi-Source Molecular Data. Bioinformatics advance access: 10.1093/bioinformatics/btw324.

See Also

showVarExplained,showHeatmaps,showPCA

Examples

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##Load JIVE results (using default settings) for simulated data 
##as in Section 2.4 of Lock et al., 2013,
##with rank 1 joint structure, and rank 1 individual structure for each dataset
data(SimResults) 
# Visualize results
# Bar plot of variation explained
plot(Results)
# Heatmap
plot(Results,type="heat")
# Principal compontents plots
plot(Results,type="pca",1,c(1,1))

r.jive documentation built on May 30, 2017, 6:31 a.m.