## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----include = FALSE----------------------------------------------------------
library(orthGS)

## ----eval=FALSE, include=TRUE-------------------------------------------------
# # # Plot species tree:
# # str <- ape::read.tree(text = "((((Pa,Psm),(Pp,Pin)),(Abi,Ap)),((Ara,(Pod,Nag)),(Sci,(Tba,Tax))));")
# # plot(str)
# # # Load GS sequence data:
# # agf <- agf
# # # Aligning sequences and building an unrooted tree
# # # (Remember you need the MUSCLE software in your path):
# # conif <- agf[which(agf$short %in% str$tip.label), ]
# # ptr <- mltree(msa(sequences = conif$prot, ids = conif$phylo_id)$ali)$tree
# #
# # # Now, we root the tree:
# # ptr <- madRoot(ptr)
# # plot(ptr, use.edge.length = FALSE, cex = 0.6)

## -----------------------------------------------------------------------------
data <- subsetGS(sp = c("Ap", "Abi", "Pin", "Pp", "Psm", "Pa"))[, 2:9]
data$phylo_id

## ----eval=FALSE, include=TRUE-------------------------------------------------
# o <- orthG(set = c("Ap", "Abi", "Pin", "Pp", "Psm", "Pa"))
# A <- o[[1]] # Adjacency matrix
# g <- o[[2]] # igraph object (orthology network)

## ----include=FALSE------------------------------------------------------------
g <- orthG(set = c("Ap", "Abi", "Pin", "Pp", "Psm", "Pa"))[[2]] 

## ----eval = FALSE-------------------------------------------------------------
# gs1a <- data$phylo_id[grepl("GS1a", data$phylo_id)] # selected nodes
# plot(igraph::subgraph(g, vids = gs1a))

## ----eval=FALSE, include=TRUE-------------------------------------------------
# data <- sdf
# gs1a <- data[which(data$gs == "GS1a" & data$tax_group != "Ferns"), ]

## ----eval = FALSE, include = TRUE---------------------------------------------
# o <- orthG()
# g <- o[[2]]
# plot(igraph::subgraph(g, vids = gs1a$Sec.Name_))