consensusMap {neatmaps}

Create Heatmaps of Consensus Matrices

Description

consensusMap produces a list of heatmaps from the consensus matrices produced during the consensus clustering step of the neatmap function.

Usage

consensusMap(neatmap_res, link_method = "average")

Arguments

neatmap_res

Output from the neatmap function.

link_method

The agglomeration method to be used for hierarchical clustering. Defaults to the average linkage method. See other methods in hclust.

Details

This function will create a list of heatmaps of the consensus matrices produced during the consensus clustering step of the neatmap function. The default clustering method used in the heatmaps is hierarchical clustering using the average linkage method, though other linkage methods can be used. The consensus cluster matrix is used as a measure of similarity. The heatmaps are produced using heatmaply.

Value

Returns of a list of heatmaps depicting the consensus matrices of each

Author(s)

Philippe Boileau, [e-mail]

References

For more information on the consensus matrices, see Monti et al..

Examples

# create the data frame using the network, node and edge attributes
df <- netsDataFrame(network_attr_df,
                    node_attr_df,
                    edge_df)

# run the neatmap code on df
neat_res <- neatmap(df, scale_df = "ecdf", max_k = 3, reps = 100, 
                    xlab = "vars", ylab = "nets", xlab_cex = 1, ylab_cex = 1)
                    
# create the list of heatmaps for each iteration
hm_list <- consensusMap(neat_res)