Get the dendrogram stored in a ModularExperiment

Get the dendrogram stored in a ModularExperiment

Usage

# S4 method for class 'ModularExperiment'
dendrogram(object)

# S4 method for class 'ModularExperiment'
dendrogram(object) <- value

Arguments

object

A ModularExperiment object.

value

New value to replace existing dendrogram.

Value

Returns a dendrogram describing relationships between genes. Usually produced through hierarchical clustering using the blockwiseModules function.

See also

WGCNA::blockwiseModules(), stats::hclust()

Author

Jack Gisby

Examples

# Create ModularExperiment with random data (100 features, 50 samples,
# 10 modules)
me <- ReducedExperiment:::.createRandomisedModularExperiment(100, 50, 10)
me
#> class: ModularExperiment 
#> dim: 100 50 10 
#> metadata(0):
#> assays(1): normal
#> rownames(100): gene_1 gene_2 ... gene_99 gene_100
#> rowData names(0):
#> colnames(50): sample_1 sample_2 ... sample_49 sample_50
#> colData names(0):
#> 10 components

# The dendrogram is usually produced during module discovery, but we can
# assign any dendrogram to the slot. Let's do hierarchical clustering on the
# features in our object and assign it
dendrogram(me) <- hclust(dist(assay(me)))
dendrogram(me)
#> 
#> Call:
#> hclust(d = dist(assay(me)))
#> 
#> Cluster method   : complete 
#> Distance         : euclidean 
#> Number of objects: 100 
#> 

# Can use default plotting approach
plot(dendrogram(me))


# Or class method that calls WGCNA::plotDendroAndColors
plotDendro(me)