consensusMap function

Create Heatmaps of Consensus Matrices

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

function.

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.

Returns

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

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.

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)

References

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

Author(s)

Philippe Boileau, philippe_boileau@berkeley.edu