In cosmonet-package/COSMONET: Screening-network Cox methods for survival analysis

# write.table(beta.bmd, file="BMD_GEO.txt", col.names = FALSE) # https://www.schemecolor.com/blue-green-red-pastels.php 
# required visNetwork, flexdashboard, igraph, graph from bioconductor, randomcolorR
# load functions to generate the network
source("../R/SupportingFunctionsGenerateNetwork.R")

# load the data
ListOfGenes <- params$inputFile
# Does your list of Genes has Headers? True or False. 
ListHeader <-  params$headerFile; # TRUE;
# disease ID 
diseaseID <- params$diseaseID; 
# node colours
genesColours <- params$nodesColours # c('#ffd9b3', '#d7fcb5', '#e4b5fc')
# select the genes corresponding to non-zero beta
non_zero_genes <- select_non_zero_genes(ListOfGenes, ListHeader)
# retrieve KEGG Information on the selected genes
genes_Pathways_matrix <- from_data_to_pathways(non_zero_genes, ListHeader)
# create network
network <- create_network(genes_Pathways_matrix$connected_genes, genes_Pathways_matrix$tot_paths, repos$gname, repos$gvalue)
g <- network$network
# set genes names
genes <- V(g)$name
if(length(V(g)$name)!=0){
  # set nodes colour
n_formatting <- define_node_colour(genes, repositoryDisease, diseaseID, genesColours)
n_colours <- n_formatting$n_colours
n_borders <- n_formatting$n_borders

shapes <- rep("ellipse", length(genes))
# Define Nodes properties
compg.nodes <- as.data.frame(list(genes,genes, n_colours, shapes, n_colours,n_borders ))
colnames(compg.nodes)<-c("id", "label", "color.background", "shape", "color.highlight.background", "color.border")

# define edges properties
compg.edges <- as.data.frame(get.edgelist(g))
compg.edges[,3:4] <- c(network$edge_number, network$edge_colour)
compg.edges[,5] <- network$edge_path
colnames(compg.edges) <- c("from", "to", "label", "color", "title")
}

Not-Isolated Genes {data-icon="fa-table"}

Row

KEGG Network

if(length(V(g)$name)!=0){
  # Visualise Nodes Legend
  legendNodes <- data.frame(id = 1:3, label = c("Mapped Up", "Mapped Down", "Not Mapped"), color = params$nodesColours, color.border =   c("#FFFFFF", "#FFFFFF","#FFFFFF"), shape = c("ellipse","ellipse","ellipse"))
  # list legend nodes
  listLegendNodes <- list(
  list(label = "Mapped Up", shape = "ellipse",
       color = list(background = params$nodesColours[1], border = "#FFFFFF")),
       #shapeProperties = list(borderDashes = list(8, 5))),
  list(label = "Mapped Down", shape = "ellipse",
       color = list(background = params$nodesColours[2], border = "#FFFFFF")),
  list(label = "Not Mapped", shape = "ellipse",
       color = list(background = params$nodesColours[3], border = "#dfe5f0"))
  )

  # Visualise Network
  visNetwork(compg.nodes, compg.edges)%>%
  visNodes(physics = FALSE, font=list(size=20), size = 30) %>%
  visIgraphLayout(layout = "layout_in_circle") %>%
  visEdges(smooth = list(enabled = T, type = 'dynamic', physics = FALSE), font = list(size=18, color = network$edge_colours)) %>%
  visLegend(useGroups = F, addNodes = listLegendNodes, width = 0.2, stepY = 50) %>%
  visPhysics(solver = "barnesHut",
            barnesHut = list(springConstant = 0.04)) %>%#0.002
  visExport(type = "pdf", name = "Partial-Network")
} else {
  print(sprintf("COSMONET has identified %d genes, but they do not share any KEGG pathways.", dim(non_zero_genes)[1]));
  print("Please check the other tab to see the Full Network of isolated genes")
}

Legend {data-width=300, data-padding=0}

if(length(V(g)$name)!=0){
plot_legend(network$legend)
# save network$legend as R file to modify it and add it to the final image for publications
legend <- network$legend
save(legend, file="legend.RData")
}

Full Network {data-icon="fa-th"}

All Genes

#load full list of genes
genes <- non_zero_genes[,1]
# find the new isolated genes to be added to the network
if(length(V(g)$name)==0){
  isolatedGenes <- genes
} else{
  isolatedGenes <- genes[-match(V(g)$name, genes)]
}
# set nodes colour
n_formatting <- define_node_colour(genes, repositoryDisease, diseaseID, genesColours)
n_colours <- n_formatting$n_colours
n_borders <- n_formatting$n_borders
shapes <- rep("ellipse", length(genes))

  listLegendNodes <- list(
  list(label = "Mapped Up", shape = "ellipse", 
       color = list(background = params$nodesColours[1], border = "#FFFFFF")),
       #shapeProperties = list(borderDashes = list(8, 5))),
  list(label = "Mapped Down", shape = "ellipse", 
       color = list(background = params$nodesColours[2], border = "#FFFFFF")),
  list(label = "Not Mapped", shape = "ellipse", 
       color = list(background = params$nodesColours[3], border = "#dfe5f0"))
  )

# Define Nodes
Nodes <- as.data.frame(list(genes,genes, n_colours, shapes, n_colours, n_borders))
colnames(Nodes)<-c("id", "label", "color.background", "shape", "color.highlight.background", "color.border")
# }
# set nodes legend
nodesLegend <- data.frame(id = 1:3, label = c("Mapped Up", "Mapped Down", "Not Mapped"), color = params$nodesColours, shape = c("ellipse","ellipse","ellipse"), color.border = c("#FFFFFF", "#FFFFFF","#e6e4df")) # no border and grey

if(length(V(g)$name)==0){
  dummyEdge <- data.frame(isolatedGenes[1],isolatedGenes[2], "#FFFFFF", "NULL")
  colnames(dummyEdge) <- c("from", "to", "color", "title")
  compg.edges <- dummyEdge
}

visNetwork(Nodes, compg.edges)%>%
  visNodes(physics = FALSE, font=list(size=20), size = 30) %>%
  # visIgraphLayout(layout = "layout_in_circle") %>%
  visIgraphLayout(layout = "layout_nicely") %>%
  visEdges(smooth = list(enabled = T, type = 'dynamic', physics = FALSE), font = list(size=18, color = network$edge_colours)) %>%
  visLegend(useGroups = F, addNodes = listLegendNodes, width = 0.2, stepY = 50) %>%
  visPhysics(solver = "barnesHut", 
            barnesHut = list(springConstant = 0.04)) %>% #0.002
 visExport(type = "pdf", name = "Full-Network")