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# file dna/R/AllShow.R
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 or 3 of the License
# (at your option).
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
#
setMethod("show","modules",
function(object){
F=slot(object,"module")
mF=length(levels(F))-(0%in%levels(F))
if (is.null(names(F)))
names(F)=paste("Gene ",1:length(F),sep="")
else{
NAnames=which(is.na(names(F)))
names(F)[NAnames]=paste("Gene ",NAnames,sep="")
}
if (mF>0){
for (i in 1:mF){
cat(paste("Module ",i,":",sep=""),"\n")
cat(names(F[F==i]),sep=",",fill=80)
cat("\n")
}
}
else{
cat("No modules\n")
}
})
setMethod("show","pairOfNetworks",
function(object){
cat("Class: pairOfNetworks\n")
N1=slot(object,"network1")
N2=slot(object,"network2")
cat("Network 1:",nrow(N1),"subjects and",ncol(N1),"genes.\n")
cat("Network 2:",nrow(N2),"subjects and",ncol(N2),"genes.\n")
if ((!is.null(colnames(N1)))&(!is.null(colnames(N2)))){
n.common=length(intersect(colnames(N1),colnames(N2)))
if ((n.common<ncol(N1))|(n.common<ncol(N2)))
if (n.common!=1){
cat("The networks have",length(intersect(colnames(N1),colnames(N2))),"genes in common.\n")
}
else{
cat("The networks have 1 gene in common.\n")
}
}
})
setMethod("show","resultsClassTest",
function(object){
cat("Tests for differential connectivity of a class of genes\n\n")
p.val=slot(object,"p.value")
delta=slot(object,"delta")
genelist=slot(object,"class.genes")
cat("Class of genes:\n")
cat(genelist,sep=",",fill=80)
cat("\n")
cat("Test statistic: delta=",delta,"\n")
cat("P-value=",p.val,"\n")
})
setMethod("show","resultsIndTest",
function(object){
cat("Tests for differential connectivity of individual genes\n")
cat("(Up to 20 most significant genes)\n\n")
p.val=slot(object,"p.values")
test.stat=slot(object,"d")
gene.names=names(p.val)
p=length(p.val)
out=data.frame(gene=gene.names,d=test.stat,p.value=p.val)
print(out[order(p.val)[1:min(p,20)],],row.names=FALSE)
})
setMethod("show","resultsModTest",
function(object){
cat("Tests for differential modular structure in two networks of genes\n\n")
p.val=slot(object,"p.value")
N=slot(object,"N")
mod1=slot(object,"modules1")
mod2=slot(object,"modules2")
cat("Network 1:\n")
summary(mod1)
cat("\n")
cat("Network 2:\n")
summary(mod2)
cat("\n")
cat("Test statistic: N=",N,"\n")
cat("P-value=",p.val,"\n")
})
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