tcell-net.R
In GeneNet: Modeling and Inferring Gene Networks

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#' ---
#' title: "T-Cell Network"
#' output: pdf_document
#' author: ""
#' date: Example for GeneNet 1.2.13 (August 2015) or later
#' ---

#' This note reproduces the “T-Cell” network example from 
#' R. Opgen-Rhein and K. Strimmer. 2006a.  *Using regularized dynamic
#' correlation to infer gene dependency networks from time-series 
#' microarray data.*  Proceedings of WCSB 2006 (June 12-13, 2006, 
#' Tampere, Finland) and R. Opgen-Rhein  and K. Strimmer. 2006b. 
#' *Inferring gene dependency networks from genomic longitudinal data: 
#' a functional data approach.* REVSTAT **4**:53-65. 
#' (http://www.ine.pt/revstat/pdf/rs060103.pdf)


#'
#' # Load GeneNet library
library("GeneNet")

#' get T cell data 
data(tcell)
tc44 = combine.longitudinal(tcell.10, tcell.34)

#'
#' # Estimate partial correlations

pc1 = ggm.estimate.pcor(tc44, lambda=0)                   # static, no shrinkage
pc2 = ggm.estimate.pcor(tc44, method="dynamic", lambda=0) # dynamic, no shrinkage
pc3 = ggm.estimate.pcor(tc44)                             # static, with shrinkage         
pc4 = ggm.estimate.pcor(tc44, method="dynamic")           # dynamic, with shrinkage


#'
#' # Find significant edges

#' We use as selection criterion local fdr <= 0.2
#'  

#' static, no shrinkage
t1.edges = network.test.edges(pc1)
t1.net = extract.network(t1.edges) # prob > 0.8
t1.net

#' dynamic, no shrinkage
t2.edges = network.test.edges(pc2)
t2.net = extract.network(t2.edges) # prob > 0.8
t2.net

#' static, with shrinkage
t3.edges = network.test.edges(pc3)
t3.net = extract.network(t3.edges) # prob > 0.8
t3.net

#' dynamic, with shrinkage
t4.edges = network.test.edges(pc4)
t4.net = extract.network(t4.edges) # prob > 0.8
t4.net


#'
#' # Produce plots using graph and Rgraphviz

library("Rgraphviz") 

node.labels = colnames(tc44)
gr1 = network.make.graph( t1.net, node.labels) 
gr2 = network.make.graph( t2.net, node.labels)  
gr3 = network.make.graph( t3.net, node.labels) 
gr4 = network.make.graph( t4.net, node.labels)  

globalAttrs = list()
globalAttrs$edge <- list(color = "blue", lty = "solid", lwd = 1, arrowsize=1)
globalAttrs$node <- list(fillcolor = "lightyellow", shape = "ellipse", fixedsize = FALSE)

edgeAttrs1 <- list()
edgeAttrs1$dir =  edge.info(gr1)$dir
edgeAttrs2 <- list()
edgeAttrs2$dir =  edge.info(gr2)$dir
edgeAttrs3 <- list()
edgeAttrs3$dir =  edge.info(gr3)$dir
edgeAttrs4 <- list()
edgeAttrs4$dir =  edge.info(gr4)$dir


#+ fig.width=8, fig.height=7
par(mfrow=c(2,2))
plot(gr1, main="Static, no shrinkage", attrs = globalAttrs, edgeAttrs = edgeAttrs1, "fdp")
plot(gr2, main="Dynamic, no shrinkage", attrs = globalAttrs, edgeAttrs = edgeAttrs2,"fdp")
plot(gr3, main="Static, with shrinkage", attrs = globalAttrs, edgeAttrs = edgeAttrs3, "fdp")
plot(gr4, main="Dynamic, with shrinkage", attrs = globalAttrs, edgeAttrs = edgeAttrs4, "fdp")
par(mfrow=c(1,1))