## ---- warning=FALSE, message=FALSE---------------------------------------
library('TreeExp')
## ---- warning=FALSE, message=FALSE---------------------------------------
data('primatexp')
data('trees')
## ---- warning=FALSE, message=FALSE---------------------------------------
dismat <- expdist(primatexp.objects, taxa = "all",
subtaxa = "brain", method = "sou")
primate_tree <- primatetimetree
primate_tree$tip.label <- colnames(dismat)
# make sure their names are the same
exp_tree <- map.ls(primate_tree, dismat)
# map the expression distance onto the primate time tree
exp_tree <- root(exp_tree, outgroup = "Macaque_Brain", resolve.root = T)
exp_tree <- no0br(exp_tree)
# make a little tweak to the expression tree,
# and make sure it is rooted and has no zero branch length
## ---- warning=FALSE, message=FALSE---------------------------------------
var_mat <- varMatInv(objects = primatexp.objects,phy = exp_tree,
taxa = "all", subtaxa = "Brain")
## ---- warning=FALSE, message=FALSE---------------------------------------
exp_table <- exptabTE(primatexp.objects,
taxa = "all", subtaxa = "Brain")
MAG_expression <- exp_table[which(rownames(exp_table) == "ENSG00000105695"),]
## ---- warning=FALSE, message=FALSE---------------------------------------
MAG_anc <- aee(MAG_expression, exp_tree, var_mat, select = "all")
## ---- warning=FALSE, message=FALSE, fig.height=4, fig.width=6------------
primate_tree$node.label <- sprintf("%.4f",MAG_anc$est)
primate_tree$tip.label <- paste0(exp_tree$tip.label, " ",
sprintf("%.4f", MAG_expression))
plot(primate_tree, edge.color = "grey80", edge.width = 4,
show.node.label = T, align.tip.label = T)
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