Required Software
dendroNetwork uses RCy3 (https://www.bioconductor.org/packages/release/bioc/html/RCy3.html)
to connect with Cytoscape and visualize networks. Cytoscape is open
source software and platform independent and provides easy visual access
to complex networks, including the attributes of both nodes and edges in
a network (see the Cytoscape-website
for more information). You will need to install and launch
Cytoscape:
To check if Cytoscape if completely loaded please run:
cytoscapePing()
Creation of networks
The creation of dendrochronological networks is done in R using the
dendroNetwork package (see readme or the vignette dendroNetwork: how to use it.
library(dendroNetwork)
data(hol_rom) # 1
sim_table_hol <- sim_table(hol_rom) # 2
g_hol <- dendro_network(sim_table_hol) # 3
g_hol_gn <- gn_names(g_hol) # 4
hol_com_cpm_all <- find_all_cpm_com(g_hol) # 5
After the networks are created, the next step would be to visualize
these in Cytoscape.
Networks in Cytoscape
To visualise a dendrochronological network in Cytoscape:
cyto_create_graph(g_hol, CPM_table = hol_com_cpm_all, GN_table = g_hol_gn)
This results in Cytoscape as the following:
Network g_hol in Cytoscape.
The next step would be to add styles for visualisation. However,
Cytoscape comes with a lot of default styles that can be confusing.
Therefore it is recommended to use once in each session:
It is not possible to visualize the styles for example for the Girvan
Newman Algorithm:
cyto_create_gn_style(g_hol)
This results in Cytoscape as the following:
The network g_hol with the Girvan Newman
communities visualized in Cytoscape
Visualizing the Clique Percolation communities in Cytoscape for the
network could be done using
cyto_create_cpm_style(g_hol, k=3, com_k = hol_com_cpm_all)
However, this would make not much sense in this example, since there
is only one full clique with k=3 .