R/graph_design.R

In thomazbastiaanssen/anansi: Annotation-Based Analysis of Specific Interactions

# Used for manuscript figure
# DiagrammeR::grViz('digraph {
#
#   graph [fontsize=10 fontname="Verdana" compound = true rankdir = LR];
#   node [shape=record fontsize=10 fontname="Verdana" style = filled layout=fdp];
#
#   data1 [label = "Dataset Y", shape = folder, fillcolor = Beige];
#
#   data2 [label = "Dataset X\n(optional)", shape = folder, fillcolor = Beige];
#
#   data3 [label = "Dictionary", shape = folder, fillcolor = Beige];
#
#   subgraph clusterWeaveWeb {
#     "Filter and\ncheck input" "Return Web"
#
#     subgraph clusterCluster {
#       "Interaction\nmode" "Membership\nmode"
#
#       label = "Generate binary\nadjacency matrix";
#       color=blue;
#     }
#
#     label = "Create a web object with\nweaveWebFromTables()";
#     color=blue;
#   }
#
#   data4 [label = "anansiWeb\nobject", shape = folder, fillcolor = Beige];
#
#   subgraph cluster_1 {
#
#     "Check call" "Pairwise\nassociations" "Differential\nassociations"
#     subgraph cluster_diff {
#     node [style=filled];
#     label = "Differential association\ntesting options";
#     color=blue;
#
#     subgraph cluster_model_type {
#     label = "Model types";
#     color=blue
#     "linear model" "linear mixed\neffects model"} ->
#     subgraph cluster_model_Structure {
#     label = "Model structure";
#     color=blue;
#     "Classical\nY ~ X" "Log-ratio\nlog(Y/X)"}
#
#     }
#     subgraph cluster_ass {
#     node [style=filled];
#     label = "Pairwise association\ntesting options";
#     color=blue;
#     "Between dataset\n(correlation)" "Within dataset\n(propr)"}
#     label = "Run analysis in the main function\nanansi()";
#     color=blue;
#     "Collect results" "Account for\nFDR" "Return Yarn"  }
#
#
#   data5 [label = "anansiYarn\nobject", shape = folder, fillcolor = Beige];
#
#   subgraph cluster_2 {
#     node [style=filled];
#     "spinToWide()" "spinToLong()" "spinToPlots()";
#     label = "Parse output to\nhandy formats";
#     color=blue;
#   }
#
#
#
#   "Plot all\nassociations"[shape = oval, fillcolor = lightblue]
#
#   "Plot individual\nassociations"[shape = oval, fillcolor = lightblue]
#
#   "Export as table"[shape = oval, fillcolor = lightblue]
#
# //Start graphing
#
#   {data1 data2 data3} -> "Filter and\ncheck input"
#
#
#   "Filter and\ncheck input" -> {"Membership\nmode" "Interaction\nmode"} -> "Return Web";
#   "Check call" -> {"Pairwise\nassociations" "Differential\nassociations"}
#
#   "Differential\nassociations" -> {"linear model" "linear mixed\neffects model"}
#   {"Classical\nY ~ X" "Log-ratio\nlog(Y/X)"} -> "Collect results"
#   "Pairwise\nassociations"      -> {"Between dataset\n(correlation)" "Within dataset\n(propr)"} -> "Collect results"
#
#   "Collect results" -> "Account for\nFDR" -> "Return Yarn" -> "data5"
#
#   "spinToLong()"  -> "Plot all\nassociations"
#   "spinToPlots()" -> "Plot individual\nassociations"
#   "spinToWide()"  -> "Export as table"
#
#   // Edges that directly connect one cluster to another
#   "data4" -> "Check call" [lhead=cluster_1];
#   "Return Web" -> "data4" [ltail=cluster_0];
#
#
#  {"data5"} -> {"spinToLong()"} [ltail=cluster_1 lhead=cluster_2];
#
# }')
#