Hierarchichal Clustering of Link Communities
getClusterRelatedness.RdThis function hierarchically clusters the link communities themselves and returns an object of class hclust.
getClusterRelatedness(x, clusterids = 1:x$numbers[3], hcmethod = "ward.D", cluster = TRUE, plot = TRUE, cutat = NULL, col = TRUE, pal = brewer.pal(11, "Spectral"), labels = FALSE, plotcut = TRUE, right = TRUE, verbose = TRUE, ...)
Arguments
| x | An object of class |
|---|---|
| clusterids | An integer vector of community IDs. Defaults to all communities. |
| hcmethod | A character string naming the hierarchical clustering method to use. Can be one of |
| cluster | Logical, whether to cluster the communities. If FALSE, the function returns the upper triangular dissimilarity matrix as a vector. Defaults to TRUE. |
| plot | Logical, whether to plot the cluster dendrogram. |
| cutat | A numerical value at which to cut the dendrogram. If NULL, the dendrogram is not cut and meta-communities are not returned. Defaults to NULL. |
| col | Logical, whether to colour the dendrogram. Defaults to TRUE. |
| pal | A character vector describing a colour palette to be used for colouring the meta-communites in the dendrogram plot. Defaults to |
| labels | Logical, whether to add labels to the dendrogram plot. |
| plotcut | Logical, whether to display a horizontal line where the dendrogram is cut. Defaults to TRUE. |
| right | Logical, whether to orient the dendrogram to the right. Defaults to TRUE. |
| verbose | Logical, whether to display the progress of the calculation on the screen. Defaults to TRUE. |
| ... | Additional arguments to be passed to |
Details
Extracting meta-communities allows the user to explore community relatedness and structure at higher levels. Community relatedness is calculated using the Jaccard coefficient and the number of nodes that community i and j share: $$S(i,j)=\frac{|n_{i}\cap n_{j}|}{|n_{i}\cup n_{j}|}$$
Value
Either a numerical vector (the upper triangular dissimilarity matrix - if cluster = FALSE), a list of integer vectors (the meta-communities - if cutat is not NULL), or an object of class hclust (if cluster is TRUE and cutat is NULL).
References
Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.
Author
Alex T. Kalinka alex.t.kalinka@gmail.com
See also
Examples
#> Checking for loops and duplicate edges... 0.000% Checking for loops and duplicate edges... 2.174% Checking for loops and duplicate edges... 4.348% Checking for loops and duplicate edges... 6.522% Checking for loops and duplicate edges... 8.696% Checking for loops and duplicate edges... 10.870% Checking for loops and duplicate edges... 13.043% Checking for loops and duplicate edges... 15.217% Checking for loops and duplicate edges... 17.391% Checking for loops and duplicate edges... 19.565% Checking for loops and duplicate edges... 21.739% Checking for loops and duplicate edges... 23.913% Checking for loops and duplicate edges... 26.087% Checking for loops and duplicate edges... 28.261% Checking for loops and duplicate edges... 30.435% Checking for loops and duplicate edges... 32.609% Checking for loops and duplicate edges... 34.783% Checking for loops and duplicate edges... 36.957% Checking for loops and duplicate edges... 39.130% Checking for loops and duplicate edges... 41.304% Checking for loops and duplicate edges... 43.478% Checking for loops and duplicate edges... 45.652% Checking for loops and duplicate edges... 47.826% Checking for loops and duplicate edges... 50.000% Checking for loops and duplicate edges... 52.174% Checking for loops and duplicate edges... 54.348% Checking for loops and duplicate edges... 56.522% Checking for loops and duplicate edges... 58.696% Checking for loops and duplicate edges... 60.870% Checking for loops and duplicate edges... 63.043% Checking for loops and duplicate edges... 65.217% Checking for loops and duplicate edges... 67.391% Checking for loops and duplicate edges... 69.565% Checking for loops and duplicate edges... 71.739% Checking for loops and duplicate edges... 73.913% Checking for loops and duplicate edges... 76.087% Checking for loops and duplicate edges... 78.261% Checking for loops and duplicate edges... 80.435% Checking for loops and duplicate edges... 82.609% Checking for loops and duplicate edges... 84.783% Checking for loops and duplicate edges... 86.957% Checking for loops and duplicate edges... 89.130% Checking for loops and duplicate edges... 91.304% Checking for loops and duplicate edges... 93.478% Checking for loops and duplicate edges... 95.652% Checking for loops and duplicate edges... 97.826% Checking for loops and duplicate edges... 100.000% #> Found and removed 4 loop(s) #> Found and removed 2 duplicate edge(s) #> Calculating edge similarities for 41 edges... 0.00% Calculating edge similarities for 41 edges... 2.56% Calculating edge similarities for 41 edges... 5.13% Calculating edge similarities for 41 edges... 7.69% Calculating edge similarities for 41 edges... 10.26% Calculating edge similarities for 41 edges... 12.82% Calculating edge similarities for 41 edges... 15.38% Calculating edge similarities for 41 edges... 17.95% Calculating edge similarities for 41 edges... 20.51% Calculating edge similarities for 41 edges... 23.08% Calculating edge similarities for 41 edges... 25.64% Calculating edge similarities for 41 edges... 28.21% Calculating edge similarities for 41 edges... 30.77% Calculating edge similarities for 41 edges... 33.33% Calculating edge similarities for 41 edges... 35.90% Calculating edge similarities for 41 edges... 38.46% Calculating edge similarities for 41 edges... 41.03% Calculating edge similarities for 41 edges... 43.59% Calculating edge similarities for 41 edges... 46.15% Calculating edge similarities for 41 edges... 48.72% Calculating edge similarities for 41 edges... 51.28% Calculating edge similarities for 41 edges... 53.85% Calculating edge similarities for 41 edges... 56.41% Calculating edge similarities for 41 edges... 58.97% Calculating edge similarities for 41 edges... 61.54% Calculating edge similarities for 41 edges... 64.10% Calculating edge similarities for 41 edges... 66.67% Calculating edge similarities for 41 edges... 69.23% Calculating edge similarities for 41 edges... 71.79% Calculating edge similarities for 41 edges... 74.36% Calculating edge similarities for 41 edges... 76.92% Calculating edge similarities for 41 edges... 79.49% Calculating edge similarities for 41 edges... 82.05% Calculating edge similarities for 41 edges... 84.62% Calculating edge similarities for 41 edges... 87.18% Calculating edge similarities for 41 edges... 89.74% Calculating edge similarities for 41 edges... 92.31% Calculating edge similarities for 41 edges... 94.87% Calculating edge similarities for 41 edges... 97.44% Calculating edge similarities for 41 edges... 100.00% #> Hierarchical clustering of edges... #> Calculating link densities... 0.00% Calculating link densities... 2.56% Calculating link densities... 5.13% Calculating link densities... 7.69% Calculating link densities... 10.26% Calculating link densities... 12.82% Calculating link densities... 15.38% Calculating link densities... 17.95% Calculating link densities... 20.51% Calculating link densities... 23.08% Calculating link densities... 25.64% Calculating link densities... 28.21% Calculating link densities... 30.77% Calculating link densities... 33.33% Calculating link densities... 35.90% Calculating link densities... 38.46% Calculating link densities... 41.03% Calculating link densities... 43.59% Calculating link densities... 46.15% Calculating link densities... 48.72% Calculating link densities... 51.28% Calculating link densities... 53.85% Calculating link densities... 56.41% Calculating link densities... 58.97% Calculating link densities... 61.54% Calculating link densities... 64.10% Calculating link densities... 66.67% Calculating link densities... 69.23% Calculating link densities... 71.79% Calculating link densities... 74.36% Calculating link densities... 76.92% Calculating link densities... 79.49% Calculating link densities... 82.05% Calculating link densities... 84.62% Calculating link densities... 87.18% Calculating link densities... 89.74% Calculating link densities... 92.31% Calculating link densities... 94.87% Calculating link densities... 97.44% Calculating link densities... 100.00% #> Maximum partition density = 0.2601626 #> Finishing up...1/4... 12% Finishing up...1/4... 25% Finishing up...1/4... 37% Finishing up...1/4... 50% Finishing up...1/4... 62% Finishing up...1/4... 75% Finishing up...1/4... 87% Finishing up...1/4... 100% Finishing up...2/4... 12% Finishing up...2/4... 25% Finishing up...2/4... 37% Finishing up...2/4... 50% Finishing up...2/4... 62% Finishing up...2/4... 75% Finishing up...2/4... 87% Finishing up...2/4... 100% Finishing up...3/4... 12% Finishing up...3/4... 25% Finishing up...3/4... 37% Finishing up...3/4... 50% Finishing up...3/4... 62% Finishing up...3/4... 75% Finishing up...3/4... 87% Finishing up...3/4... 100% Finishing up...4/4... 0.00% Finishing up...4/4... 4.76% Finishing up...4/4... 9.52% Finishing up...4/4... 14.29% Finishing up...4/4... 19.05% Finishing up...4/4... 23.81% Finishing up...4/4... 28.57% Finishing up...4/4... 33.33% Finishing up...4/4... 38.10% Finishing up...4/4... 42.86% Finishing up...4/4... 47.62% Finishing up...4/4... 52.38% Finishing up...4/4... 57.14% Finishing up...4/4... 61.90% Finishing up...4/4... 66.67% Finishing up...4/4... 71.43% Finishing up...4/4... 76.19% Finishing up...4/4... 80.95% Finishing up...4/4... 85.71% Finishing up...4/4... 90.48% Finishing up...4/4... 95.24% Finishing up...4/4... 100.00% #> Plotting... #> Colouring dendrogram... 1% Colouring dendrogram... 2% Colouring dendrogram... 3% Colouring dendrogram... 4% Colouring dendrogram... 6% Colouring dendrogram... 7% Colouring dendrogram... 8% Colouring dendrogram... 9% Colouring dendrogram... 11% Colouring dendrogram... 12% Colouring dendrogram... 13% Colouring dendrogram... 14% Colouring dendrogram... 16% Colouring dendrogram... 17% Colouring dendrogram... 18% Colouring dendrogram... 19% Colouring dendrogram... 20% Colouring dendrogram... 22% Colouring dendrogram... 23% Colouring dendrogram... 24% Colouring dendrogram... 25% Colouring dendrogram... 27% Colouring dendrogram... 28% Colouring dendrogram... 29% Colouring dendrogram... 30% Colouring dendrogram... 32% Colouring dendrogram... 33% Colouring dendrogram... 34% Colouring dendrogram... 35% Colouring dendrogram... 37% Colouring dendrogram... 38% Colouring dendrogram... 39% Colouring dendrogram... 40% Colouring dendrogram... 41% Colouring dendrogram... 43% Colouring dendrogram... 44% Colouring dendrogram... 45% Colouring dendrogram... 46% Colouring dendrogram... 48% Colouring dendrogram... 49% Colouring dendrogram... 50% Colouring dendrogram... 51% Colouring dendrogram... 53% Colouring dendrogram... 54% Colouring dendrogram... 55% Colouring dendrogram... 56% Colouring dendrogram... 58% Colouring dendrogram... 59% Colouring dendrogram... 60% Colouring dendrogram... 61% Colouring dendrogram... 62% Colouring dendrogram... 64% Colouring dendrogram... 65% Colouring dendrogram... 66% Colouring dendrogram... 67% Colouring dendrogram... 69% Colouring dendrogram... 70% Colouring dendrogram... 71% Colouring dendrogram... 72% Colouring dendrogram... 74% Colouring dendrogram... 75% Colouring dendrogram... 76% Colouring dendrogram... 77% Colouring dendrogram... 79% Colouring dendrogram... 80% Colouring dendrogram... 81% Colouring dendrogram... 82% Colouring dendrogram... 83% Colouring dendrogram... 85% Colouring dendrogram... 86% Colouring dendrogram... 87% Colouring dendrogram... 88% Colouring dendrogram... 90% Colouring dendrogram... 91% Colouring dendrogram... 92% Colouring dendrogram... 93% Colouring dendrogram... 95% Colouring dendrogram... 96% Colouring dendrogram... 97% Colouring dendrogram... 98% Colouring dendrogram... 100%## Cluster the link communities. getClusterRelatedness(lc)#> Calculating cluster similarities 1/2... 0.00% Calculating cluster similarities 1/2... 2.94% Calculating cluster similarities 1/2... 5.88% Calculating cluster similarities 1/2... 8.82% Calculating cluster similarities 1/2... 11.76% Calculating cluster similarities 1/2... 14.71% Calculating cluster similarities 1/2... 17.65% Calculating cluster similarities 1/2... 20.59% Calculating cluster similarities 1/2... 23.53% Calculating cluster similarities 1/2... 26.47% Calculating cluster similarities 1/2... 29.41% Calculating cluster similarities 1/2... 32.35% Calculating cluster similarities 1/2... 35.29% Calculating cluster similarities 1/2... 38.24% Calculating cluster similarities 1/2... 41.18% Calculating cluster similarities 1/2... 44.12% Calculating cluster similarities 1/2... 47.06% Calculating cluster similarities 1/2... 50.00% Calculating cluster similarities 1/2... 52.94% Calculating cluster similarities 1/2... 55.88% Calculating cluster similarities 1/2... 58.82% Calculating cluster similarities 1/2... 61.76% Calculating cluster similarities 1/2... 64.71% Calculating cluster similarities 1/2... 67.65% Calculating cluster similarities 1/2... 70.59% Calculating cluster similarities 1/2... 73.53% Calculating cluster similarities 1/2... 76.47% Calculating cluster similarities 1/2... 79.41% Calculating cluster similarities 1/2... 82.35% Calculating cluster similarities 1/2... 85.29% Calculating cluster similarities 1/2... 88.24% Calculating cluster similarities 1/2... 91.18% Calculating cluster similarities 1/2... 94.12% Calculating cluster similarities 1/2... 97.06% Calculating cluster similarities 2/2... 0.00% Calculating cluster similarities 2/2... 16.67% Calculating cluster similarities 2/2... 33.33% Calculating cluster similarities 2/2... 50.00% Calculating cluster similarities 2/2... 66.67% Calculating cluster similarities 2/2... 83.33% Calculating cluster similarities 2/2... 100.00% #> Hierarchical clustering... #> Plotting...#> #> Call: #> hclust(d = distobj, method = hcmethod) #> #> Cluster method : ward.D #> Number of objects: 8 #>## Cluster the link communities, cut the dendrogram, and return the meta-communities. getClusterRelatedness(lc, cutat = 1)#> Calculating cluster similarities 1/2... 0.00% Calculating cluster similarities 1/2... 2.94% Calculating cluster similarities 1/2... 5.88% Calculating cluster similarities 1/2... 8.82% Calculating cluster similarities 1/2... 11.76% Calculating cluster similarities 1/2... 14.71% Calculating cluster similarities 1/2... 17.65% Calculating cluster similarities 1/2... 20.59% Calculating cluster similarities 1/2... 23.53% Calculating cluster similarities 1/2... 26.47% Calculating cluster similarities 1/2... 29.41% Calculating cluster similarities 1/2... 32.35% Calculating cluster similarities 1/2... 35.29% Calculating cluster similarities 1/2... 38.24% Calculating cluster similarities 1/2... 41.18% Calculating cluster similarities 1/2... 44.12% Calculating cluster similarities 1/2... 47.06% Calculating cluster similarities 1/2... 50.00% Calculating cluster similarities 1/2... 52.94% Calculating cluster similarities 1/2... 55.88% Calculating cluster similarities 1/2... 58.82% Calculating cluster similarities 1/2... 61.76% Calculating cluster similarities 1/2... 64.71% Calculating cluster similarities 1/2... 67.65% Calculating cluster similarities 1/2... 70.59% Calculating cluster similarities 1/2... 73.53% Calculating cluster similarities 1/2... 76.47% Calculating cluster similarities 1/2... 79.41% Calculating cluster similarities 1/2... 82.35% Calculating cluster similarities 1/2... 85.29% Calculating cluster similarities 1/2... 88.24% Calculating cluster similarities 1/2... 91.18% Calculating cluster similarities 1/2... 94.12% Calculating cluster similarities 1/2... 97.06% Calculating cluster similarities 2/2... 0.00% Calculating cluster similarities 2/2... 16.67% Calculating cluster similarities 2/2... 33.33% Calculating cluster similarities 2/2... 50.00% Calculating cluster similarities 2/2... 66.67% Calculating cluster similarities 2/2... 83.33% Calculating cluster similarities 2/2... 100.00% #> Hierarchical clustering... #> Extracting clusters... 0.00% Extracting clusters... 25.00% Extracting clusters... 50.00% Extracting clusters... 75.00% Extracting clusters... 100.00% #> Colouring dendrogram... 6% Colouring dendrogram... 13% Colouring dendrogram... 20% Colouring dendrogram... 26% Colouring dendrogram... 33% Colouring dendrogram... 40% Colouring dendrogram... 46% Colouring dendrogram... 53% Colouring dendrogram... 60% Colouring dendrogram... 66% Colouring dendrogram... 73% Colouring dendrogram... 80% Colouring dendrogram... 86% Colouring dendrogram... 93% Colouring dendrogram... 100% #> Plotting...#> [[1]] #> [1] 2 5 #> #> [[2]] #> [1] 3 7 8 #> #> [[3]] #> [1] 1 4 6 #>
