In broadinstitute/CommunityAMARETTO: CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Run Information

DTRunInfo

Community Network Visualization

Nodes_Mnetwork<-igraph::as_data_frame(cAMARETTOnetworkM$module_network,what="vertices")

layout_1<-cAMARETTOnetworkM$layoutMN
layout_1<- norm_coords(layout_1, ymin=-1, ymax=1, xmin=-1, xmax=1)
plot(cAMARETTOnetworkC$CommGraph,
     rescale = TRUE,
     layout = layout_1*1.2,
     #layout=layout_in_circle,
     vertex.color = as.character(Nodes_Mnetwork$color),
     vertex.label = NA,
     # vertex.frame.color = NA,
     # edge.color = "gray80",
     mark.groups = cAMARETTOnetworkC$community_list,
     mark.col = cAMARETTOnetworkC$color_list
     # mark.border = NA
     )

legend(x = -1.5, y = -1.1+0.05*length(cAMARETTOnetworkM$colMN), legend = names(cAMARETTOnetworkM$colMN), col = cAMARETTOnetworkM$colMN, pch=19, bty="n",ncol=ceiling(length(cAMARETTOnetworkM$colMN)/5))
legend(x = 1.1, y = 1.5, legend=names(cAMARETTOnetworkC$color_list), col=cAMARETTOnetworkC$color_list, pch=19, bty="n",cex=max(0.9,1/(1+0.02*length(cAMARETTOnetworkC$color_list))),ncol=ceiling(length(cAMARETTOnetworkC$color_list)/15))

Assignment of Regulatory Modules Shared or Distinct across Communities and Data Sets

DTComModulesLink

broadinstitute/CommunityAMARETTO documentation built on April 6, 2020, 10:44 p.m.