linkcomm
Tools for Generating, Visualizing, and Analysing Link Communities in Networks

Package index
Search the linkcomm package
Vignettes
Functions
84
Source code
5
Man pages
43
Home
/
CRAN
/
linkcomm
/
plotLinkCommGraph: Plot a Graph Layout of Link Communities

plotLinkCommGraph: Plot a Graph Layout of Link Communities
In linkcomm: Tools for Generating, Visualizing, and Analysing Link Communities in Networks

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/linkcomm_plotting.R

Description

This function is called by plot.linkcomm to plot a graph layout of the link communities.

Usage

1
2
3
4
5
6
7
8
9
plotLinkCommGraph(x, clusterids = 1:length(x$clusters), nodes = NULL,
        layout = layout.fruchterman.reingold, pal = brewer.pal(7, "Set2"),
        random = TRUE, node.pies = TRUE, pie.local = TRUE, vertex.radius = 0.03,
        scale.vertices = 0.05, edge.color = NULL, vshape = "none", vsize = 15,
        ewidth = 3, margin = 0, vlabel.cex = 0.8, vlabel.color = "black",
        vlabel.family = "Helvetica", vertex.color = "palegoldenrod",
        vlabel = TRUE, col.nonclusters = "black", jitter = 0.2, circle = TRUE,
        printids = TRUE, cid.cex = 1, shownodesin = 0, showall = FALSE,
        verbose = TRUE, ...)

Arguments

x

An object of class linkcomm.

clusterids

An integer vector of community IDs. Defaults to all communities.

nodes

A character vector naming the nodes to be plotted. If NULL, then community IDs are used instead. Defaults to NULL.

layout

A character string or function identifying the layout algorithm to be used for positioning nodes in the graph. Defaults to layout.fruchterman.reingold. See details for alternative layouts.

pal

A character vector describing a colour palette to be used for colouring the link communities in the graph. Defaults to brewer.pal(7, "Set2").

random

Logical, whether to randomise the link colours. Defaults to TRUE.

node.pies

Logical, whether to plot node pies showing as a pie chart the fraction of each node's edges which belong to each of its communities. Defaults to TRUE.

pie.local

Logical, whether to include pie segments for just the communities to which the chosen nodes belong, or for all communities. In the latter case, communities that are not present among the chosen nodes will appear as empty segments in the node pies. Will be ignored if node.pies is FALSE. Defaults to TRUE.

vertex.radius

A real number specifying the vertex radius. Defaults to 0.03. Will be ignored if node.pies is FALSE.

scale.vertices

A real number specifying the fraction of increase in vertex radius for each community membership. If NULL then all vertices are the same size. Defaults to 0.05. Will be ignored if node.pies is FALSE.

edge.color

A character string specifying the colour of edges. Defaults to "grey". Will be ignored if node.pies is FALSE.

vshape

A character string specifying the shape of the nodes. Can be one of "none", "circle", "square", "csquare", "rectangle", "crectangle", and "vrectangle". Defaults to "none".

vsize

An integer vector of node sizes. If there is a single value this will be used for all nodes. If there are multiple values, it must be the same length as the number of nodes in the network to be visualized. See graph.feature for generating these values. This argument only has an effect when vshape is not set to "none". Defaults to 15.

ewidth

An integer vector of edge widths. If there is a single value this will be used for all edges. If there are multiple values, it must be the same length as the number of edges in the network to be visualized. See graph.feature for generating these values. Defaults to 3.

margin

A numerical value specifying the amount of empty space around the graph. Negative values will zoom into the graph. Defaults to 0.

vlabel.cex

A numerical value specifying the size of node labels. Defaults to 0.8.

vlabel.color

A character string specifying the color of node labels. Defaults to "black".

vlabel.family

A character string specifying the font family for node labels. Defaults to "Helvetica".

vertex.color

A character string specifying the colour of nodes. If this is a character vector then the colours will be recycled. Defaults to "palegoldenrod".

vlabel

Logical, whether node labels are to be added. Defaults to TRUE.

col.nonclusters

A character string specifying the colour of edges that do not belong to any communities. Will only have an effect if showall is TRUE. Defaults to "black".

jitter

A numerical value specifying the range (negative to positive) of random noise that will be added to nodes that have identical x-y coordinates. Defaults to 0.2. Only used for Spencer circle layouts.

circle

Logical, whether to display a circle for a Spencer circle layout. Defaults to TRUE.

printids

Logical, whether to display community IDs at their anchor points around the Spencer circle. Defaults to TRUE.

cid.cex

A numerical value specifying the size of community IDs around the Spencer circle. Defaults to 1.

shownodesin

An integer value specifying the number of communities a node must belong to before it will be displayed. If 0 then all nodes are displayed. Defaults to 0.

showall

Logical, whether to display all links in the network regardless of whether they belong to communities or not. Defaults to FALSE.

verbose

Logical, whether to print the progress of the calculation to the screen. Defaults to TRUE.

...

Additional arguments to be passed to plot.

Details

Here we describe the parameters for plotting link community graphs using:
plot(x, type = "graph", layout = layout)

Various graph layouts are available:

  1. "spencer.circle"

  2. layout.random

  3. layout.circle

  4. layout.sphere

  5. layout.fruchterman.reingold

  6. layout.kamada.kawai

  7. layout.spring

  8. layout.reingold.tilford

  9. layout.fruchterman.reingold.grid

  10. layout.lgl

  11. layout.graphopt

  12. layout.mds

  13. layout.svd

  14. layout.norm

All of these, except the "spencer.circle", are described in more detail in the igraph package. The "spencer.circle" is described in layout.spencer.circle.

Value

A graph plot.

Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

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.

See Also

plot.linkcomm, layout.spencer.circle, graph.feature, igraph.plotting

Examples

1
2
3
4
5
6
7
8
9
## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)

## Plot a graph of link communities.
plot(lc, type = "graph")

## Plot a graph of link communities using a Spencer circle layout.
plot(lc, type = "graph", layout = "spencer.circle")

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: RColorBrewer

Welcome to linkcomm version 1.0-11

For a step-by-step guide to using linkcomm functions:
   > vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
   > demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
   > citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))


   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% 
   Getting node community edge density...4%
   Getting node community edge density...9%
   Getting node community edge density...13%
   Getting node community edge density...18%
   Getting node community edge density...22%
   Getting node community edge density...27%
   Getting node community edge density...31%
   Getting node community edge density...36%
   Getting node community edge density...40%
   Getting node community edge density...45%
   Getting node community edge density...50%
   Getting node community edge density...54%
   Getting node community edge density...59%
   Getting node community edge density...63%
   Getting node community edge density...68%
   Getting node community edge density...72%
   Getting node community edge density...77%
   Getting node community edge density...81%
   Getting node community edge density...86%
   Getting node community edge density...90%
   Getting node community edge density...95%
   Getting node community edge density...100%
   Getting node layout...
   Constructing node pies...4%
   Constructing node pies...9%
   Constructing node pies...13%
   Constructing node pies...18%
   Constructing node pies...22%
   Constructing node pies...27%
   Constructing node pies...31%
   Constructing node pies...36%
   Constructing node pies...40%
   Constructing node pies...45%
   Constructing node pies...50%
   Constructing node pies...54%
   Constructing node pies...59%
   Constructing node pies...63%
   Constructing node pies...68%
   Constructing node pies...72%
   Constructing node pies...77%
   Constructing node pies...81%
   Constructing node pies...86%
   Constructing node pies...90%
   Constructing node pies...95%
   Constructing node pies...100%
   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% 
   Getting node community edge density...4%
   Getting node community edge density...9%
   Getting node community edge density...13%
   Getting node community edge density...18%
   Getting node community edge density...22%
   Getting node community edge density...27%
   Getting node community edge density...31%
   Getting node community edge density...36%
   Getting node community edge density...40%
   Getting node community edge density...45%
   Getting node community edge density...50%
   Getting node community edge density...54%
   Getting node community edge density...59%
   Getting node community edge density...63%
   Getting node community edge density...68%
   Getting node community edge density...72%
   Getting node community edge density...77%
   Getting node community edge density...81%
   Getting node community edge density...86%
   Getting node community edge density...90%
   Getting node community edge density...95%
   Getting node community edge density...100%
   Getting node layout...
   Constructing node pies...4%
   Constructing node pies...9%
   Constructing node pies...13%
   Constructing node pies...18%
   Constructing node pies...22%
   Constructing node pies...27%
   Constructing node pies...31%
   Constructing node pies...36%
   Constructing node pies...40%
   Constructing node pies...45%
   Constructing node pies...50%
   Constructing node pies...54%
   Constructing node pies...59%
   Constructing node pies...63%
   Constructing node pies...68%
   Constructing node pies...72%
   Constructing node pies...77%
   Constructing node pies...81%
   Constructing node pies...86%
   Constructing node pies...90%
   Constructing node pies...95%
   Constructing node pies...100%

linkcomm documentation built on Feb. 4, 2021, 5:05 p.m.

Related to plotLinkCommGraph in linkcomm...

linkcomm index
Package overview

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close