Description Usage Arguments Details Author(s) References See Also Examples
plot.PCSFe
plots an interactive figure of the subnetwork
to display the functionla enrichment analysis, which is obtained by employing
enrichment_analysis
on the subnetwork.
1 2 3 4 |
x |
An output subnetwork provided by the |
edge_width |
A |
node_size |
A |
node_label_cex |
A |
Terminal_node_legend |
A |
Steiner_node_legend |
A |
... |
Ignored. |
An enrichment analysis of the final subnetwork obtained by multiple runs of the PCSF
(with random noise added edge costs) is performed by using enrichment_analysis
.
The subnetwork is clustered using an edge betweenness clustering algorithm from the
igraph package, and for each cluster functional enrichment is done by employing the
ENRICHR API (Chen et al., 2013). An interactive visualization of the final subnetwork
is plotted, where the node sizes and edge widths are proportional to the frequency of show
ups in total randomised runs. Nodes are colored according to the cluster membership, and
the top 15 functional enrichment terms are displayed in tabular format during the hover-over
of the node in that cluster. A specific cluster can be displayed separately in the figure
by selecting from the icon list at the top left side of the figure.
Murodzhon Akhmedov
Chen E.Y., Christopher M.T., Yan K., Qiaonan D., Zichen W., Gabriela V.M., Neil R.C., and Avi M. (2013) Enrichr: Interactive and Collaborative Html5 Gene List Enrichment Analysis Tool. BMC Bioinformatics 14 (1). BioMed Central: 1.
enrichment_analysis
, PCSF_rand
, plot.PCSF
1 2 3 4 5 6 7 8 9 10 | ## Not run:
library("PCSF")
data("STRING")
data("Tgfb_phospho")
terminals <- Tgfb_phospho
ppi <- construct_interactome(STRING)
subnet <- PCSF_rand(ppi, terminals, n = 10, r = 0.1, w = 2, b = 1, mu = 0.0005)
res <- enrichment_analysis(subnet)
plot(res$subnet)
## End(Not run)
|
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