Calculate Node Coordinates for a Spencer Circle
layout.spencer.circle.RdThis function returns the x-y coordinates for nodes in a Spencer circle together with community anchor positions.
layout.spencer.circle(x, clusterids = 1:x$numbers[3], verbose = TRUE, jitter = 0.2)
Arguments
| x | An object of class |
|---|---|
| clusterids | An integer vector of community IDs. Defaults to all communities. |
| verbose | Logical, whether to print the progress of the calculation to the screen. Defaults to TRUE. |
| jitter | A positive numerical value specifying the range (negative to positive) of random, uniformly distributed noise that will be added to nodes that have identical x-y coordinates. Defaults to 0.2. |
Details
This algorithm anchors communities evenly around the circumference of a circle in their dendrogram order (to minimise crossing over of links) and positions nodes within the circle according to how many links they possess in each of the communities (Spencer, 2010). Thus, nodes that have links to a lot of communities will get pushed into the centre of the circle making this method well suited for representing ego networks where one or a small number of nodes belong to multiple communities.
Value
A list with the following components:
A numerical matrix with nodes as rows and with 2 columns; the first contains the x coordinates and the second the y coordinates.
A numerical matrix with communities as rows and with 2 columns of x and y coordinates.
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.
Spencer, R. (2010). http://scaledinnovation.com/analytics/communities/comlinks.html
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%## Extract x-y coordinates for nodes in a Spencer circle. layout.spencer.circle(lc)#> Ordering communities according to dendrogram...12% Ordering communities according to dendrogram...25% Ordering communities according to dendrogram...37% Ordering communities according to dendrogram...50% Ordering communities according to dendrogram...62% Ordering communities according to dendrogram...75% Ordering communities according to dendrogram...87% Ordering communities according to dendrogram...100% #> Calculating node co-ordinates for Spencer circle...4% Calculating node co-ordinates for Spencer circle...9% Calculating node co-ordinates for Spencer circle...13% Calculating node co-ordinates for Spencer circle...18% Calculating node co-ordinates for Spencer circle...22% Calculating node co-ordinates for Spencer circle...27% Calculating node co-ordinates for Spencer circle...31% Calculating node co-ordinates for Spencer circle...36% Calculating node co-ordinates for Spencer circle...40% Calculating node co-ordinates for Spencer circle...45% Calculating node co-ordinates for Spencer circle...50% Calculating node co-ordinates for Spencer circle...54% Calculating node co-ordinates for Spencer circle...59% Calculating node co-ordinates for Spencer circle...63% Calculating node co-ordinates for Spencer circle...68% Calculating node co-ordinates for Spencer circle...72% Calculating node co-ordinates for Spencer circle...77% Calculating node co-ordinates for Spencer circle...81% Calculating node co-ordinates for Spencer circle...86% Calculating node co-ordinates for Spencer circle...90% Calculating node co-ordinates for Spencer circle...95% Calculating node co-ordinates for Spencer circle...100%#> $nodes #> [,1] [,2] #> 17 -7.071068e-01 -7.071068e-01 #> 15 -8.535534e-01 -3.535534e-01 #> 8 -6.210323e-01 -5.580547e-01 #> 16 7.071068e-01 -7.071068e-01 #> 13 5.468669e-01 -9.661282e-01 #> 10 3.535534e-01 -8.535534e-01 #> 29 4.193654e-01 -8.977278e-01 #> 14 6.123234e-17 1.000000e+00 #> 6 -5.857864e-02 7.414214e-01 #> 7 -8.368378e-02 6.306019e-01 #> 3 2.500000e-01 7.500000e-01 #> 21 -7.071068e-01 7.071068e-01 #> 12 -8.744743e-01 3.030458e-01 #> 1 -7.753799e-01 8.988965e-01 #> 26 -6.663052e-01 7.699051e-01 #> 22 -1.836970e-16 -1.000000e+00 #> 5 5.000000e-01 -5.000000e-01 #> 18 1.000000e+00 -2.449294e-16 #> 2 8.184255e-01 4.676582e-02 #> 19 1.380712e-01 4.714045e-01 #> 9 7.071068e-01 7.071068e-01 #> 25 5.394448e-01 7.694998e-01 #> #> $anchors #> [,1] [,2] #> [1,] 7.071068e-01 7.071068e-01 #> [2,] 6.123234e-17 1.000000e+00 #> [3,] -7.071068e-01 7.071068e-01 #> [4,] -1.000000e+00 1.224647e-16 #> [5,] -7.071068e-01 -7.071068e-01 #> [6,] -1.836970e-16 -1.000000e+00 #> [7,] 7.071068e-01 -7.071068e-01 #> [8,] 1.000000e+00 -2.449294e-16 #>
