plotHeatmap: Plot Heatmap for a supervised JIVE model

In enorthrop/sup.r.jive: Supervised JIVE Methods: JIVE Predict, sJIVE, and sesJIVE

Plot Heatmap for a supervised JIVE model

Description

A heat map to visually display the joint and invidual components in a fitted model.

Usage

plotHeatmap(result, ...)

## S3 method for class 'sJIVE'
plotHeatmap(result, order_by = -1, ylab = "Y", xlab = NULL, ycex = 1, ...)

## S3 method for class 'JIVEpred'
plotHeatmap(result, order_by = -1, ylab = "Y", xlab = NULL, ycex = 1, ...)

## S3 method for class 'sesJIVE'
plotHeatmap(result, order_by = -1, ylab = "Y", xlab = NULL, ycex = 1, ...)

Arguments

result	An object of class "sJIVE", "JIVEpred", "sesJIVE".
...	further arguments passed to or from other methods.
order_by	A value that specifies how to order the rows and columns of the heatmap. #If order_by=-1, orderings are determined by the outcome. 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 hierarchical clustering of Euclidean distances.
ylab	A label for the outcome dataset.
xlab	A vector with labels for each X dataset.
ycex	A scalar to change the font size of the labels.

Details

This function takes a fitted sJIVE, sesJIVE, or JIVE.pred model and plots the results using heatplots. Ensure your plotting window is sufficiently large prior to running this function to get the best results visually.

Value

A heat map.

Methods (by class)

• plotHeatmap(sJIVE):

• plotHeatmap(JIVEpred):

• plotHeatmap(sesJIVE):

Examples

data(SimData.norm)
fit <- sJIVE(X=SimData.norm$X,Y=SimData.norm$Y,
                  rankJ=1,rankA=c(1,1),eta=0.5)
plotHeatmap(fit,  ylab="outcome",
        xlab=c("Metabolomic", "Proteomic"), ycex=0.9)

data(SimData.norm)
fit <- JIVE.pred(X=SimData.norm$X,Y=SimData.norm$Y,
                  rankJ=1,rankA=c(1,1))
plotHeatmap(fit,  ylab="outcome",
        xlab=c("Metabolomic", "Proteomic"), ycex=0.9)

enorthrop/sup.r.jive documentation built on Nov. 18, 2022, 6:01 p.m.