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data(thaliana)
head(thaliana, n=3)
#Construct a path for genotype-phenotype interactions network in thaliana data
res <- netphenogeno(data = thaliana); res
plot(res)
#Select an optimal network
sel <- selectnet(res)
#Plot selected network and the conditional correlation (CI) relationships
plot(sel, vis="CI")
plot(sel, vis="CI", n.var = c(8,56,31,33,31,30), vertex.size=4)
#Visualize interactive plot of the selected network
#Color "red" for 8 phenotypes, and different colors for each chromosome.
cl <- c(rep("red", 8), rep("white",56), rep("tan1",31),
rep("gray",33), rep("lightblue2",31), rep("salmon2",30))
plot(sel, vis="interactive", vertex.color= cl)
#Partial correlations between genotypes and phenotypes in the thaliana dataset.
image(sel$par.cor, xlab="geno-pheno", ylab="geno-pheno", sub="")
# }
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