r.jive (version 2.4)

showHeatmaps: Heatmaps for JIVE Decompositions

Description

This function draws heatmaps for the components of a JIVE decomposition.

Usage

showHeatmaps(result, order_by = 0, show_all = TRUE)

Arguments

result

An object of class "jive".

order_by

Specifies how to order the rows and columns of the heatmap. If order_by=-1, the matrices are not re-ordered. If order_by=0, orderings are determined by joint structure. Otherwise, order_by gives the number of the individual structure dataset to determine the ordering. In all cases orderings are determined by complete-linkage hiearchichal clustering of Euclidean distances.

show_all

Specifies whether to show the full decomposition of the data, JIVE estimates, and noise. If show_all=FALSE, only the matrix (or matrices) that determined the column ordering is shown.

Details

The columns correspond to the shared dimension (for example, a common sample set), and the ordering of the columns is the same for all matrices shown.

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

jive, plot.jive, show.image

Examples

# NOT RUN {
##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) 
# Display the heatmaps (may need to fiddle with plot window dimensions for this to appear well)
showHeatmaps(Results)
# Order by first data set individual structure
showHeatmaps(Results, order_by=1)
# Show only joint structure
showHeatmaps(Results, show_all=FALSE)
# }