Plot Selected Features — plotFeatures • stabm

Creates a heatmap of the features which are selected in at least one feature set. The sets are ordered according to average linkage hierarchical clustering based on the Manhattan distance. If sim.mat is given, the features are ordered according to average linkage hierarchical clustering based on 1 - sim.mat. Otherwise, the features are ordered in the same way as the feature sets.

Note that this function needs the packages ggplot2, cowplot and ggdendro installed.

plotFeatures(features, sim.mat = NULL)

Arguments

features: list (length >= 2)
Chosen features per dataset. Each element of the list contains the features for one dataset. The features must be given by their names (character) or indices (integerish).
sim.mat: numeric matrix
Similarity matrix which contains the similarity structure of all features based on all datasets. The similarity values must be in the range of [0, 1] where 0 indicates very low similarity and 1 indicates very high similarity. If the list elements of features are integerish vectors, then the feature numbering must correspond to the ordering of sim.mat. If the list elements of features are character vectors, then sim.mat must be named and the names of sim.mat must correspond to the entries in features.

Value

Object of class ggplot.

Examples

feats = list(1:3, 1:4, 1:5)
mat = 0.92 ^ abs(outer(1:10, 1:10, "-"))
plotFeatures(features = feats)
#> Loading required namespace: ggplot2
#> Loading required namespace: cowplot
#> Loading required namespace: ggdendro

plotFeatures(features = feats, sim.mat = mat)