inst/doc/manuscript.R

In coglasso: Collaborative Graphical Lasso - Multi-Omics Network Reconstruction

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

## ----setup--------------------------------------------------------------------
#  library(coglasso)

## -----------------------------------------------------------------------------
#  help(multi_omics_sd)

## -----------------------------------------------------------------------------
#  nlambda_w <- 30
#  nlambda_b <- 30
#  cs <- c(0.01, 0.05, 0.1, 0.2, 1, 5, 10, 20, 100)

## -----------------------------------------------------------------------------
#  cg <- coglasso(multi_omics_sd,
#    pX = 162,
#    nlambda_w = nlambda_w,
#    nlambda_b = nlambda_b,
#    c = cs
#  )

## -----------------------------------------------------------------------------
#  set.seed(42)
#  sel_cg <- stars_coglasso(cg)

## -----------------------------------------------------------------------------
#  # To create the igraph object from the selected adjacency matrix:
#  sel_graph <- igraph::graph.adjacency(sel_cg$sel_adj, mode = "undirected")
#  
#  # Setting some graphical parameters
#  igraph::V(sel_graph)$label <- NA
#  igraph::V(sel_graph)$color <- c(rep("#00ccff", 162), rep("#ff9999", 76))
#  igraph::V(sel_graph)$frame.color <- c(rep("#002060", 162), rep("#800000", 76))
#  igraph::V(sel_graph)$frame.width <- 2
#  igraph::V(sel_graph)$size <- 4
#  igraph::E(sel_graph)$width <- 0.3
#  
#  # Setting a force-based network layout and removing disconnected nodes from the graph
#  lo <- igraph::layout_with_fr(sel_graph)
#  diconnected <- which(igraph::degree(sel_graph) == 0)
#  sel_graph2 <- igraph::delete.vertices(sel_graph, diconnected)
#  lo2 <- lo[-diconnected, ]
#  
#  # Plotting
#  plot(sel_graph2, layout = lo2)

## -----------------------------------------------------------------------------
#  igraph::V(sel_graph)$label<-colnames(sel_cg$data)
#  cirbp_index <- which(colnames(sel_cg$data) == "Cirbp")
#  subnetwork <- igraph::subgraph(
#    sel_graph,
#    c(cirbp_index, igraph::neighbors(sel_graph, cirbp_index))
#  )
#  plot(subnetwork)

## -----------------------------------------------------------------------------
#  communities <- igraph::cluster_fast_greedy(sel_graph)
#  community2 <- communities[[2]]
#  community2_graph<-igraph::subgraph(sel_graph, community2)
#  
#  # Focusing on nodes of interest
#  fosjun_erg_AA <- c("Fos", "Fosb", "Junb", "Fosl2", "Egr1", "Egr2", "Egr3", "Ala", "Arg", "Asn","His","Ile","Leu","Lys","Met","Orn","Phe","Ser","Thr","Tyr","Val")
#  igraph::V(community2_igraph)[!(label %in% fosjun_erg_AA)]$color<-c(rep("#3bd8ff", 29), rep("#ffadad", 5))
#  igraph::V(community2_igraph)[!(label %in% fosjun_erg_AA)]$frame.color<-NA
#  igraph::V(community2_igraph)[!(label %in% fosjun_erg_AA)]$label<-NA
#  
#  lo_community2 <- igraph::layout_with_fr(community2_graph)
#  plot(community2_graph, layout=lo_community2)