| showHeatmaps {r.jive} | R Documentation |
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.
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
Examples
##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)