Drawing diagram of a multiple / parallel mediation model in R

Question

I want to draw a publication-ready diagram of a parallel mediation model in R.

I adapted the Diagrammer + Graphviz Code provided here https://stackoverflow.com/questions/46465752/drawing-simple-mediation-diagram-in-r, but I do not seem to get the expected output. I think I am doing something wrong with the rank argument.

My goal is to have the predictor and outcome at the bottom and all three mediators in one vertical line above.

This following code almost gets it, but puts two mediatiors below instead on top. This would also work, if the arrow from xx to yy would at least land in the middle of the box.

med_data <-
  data.frame(
    lab_x   = "XXXXXX",
    lab_m1   = "MMMMMM 1",
    lab_m2   = "MMMMMM 2",
    lab_m3   = "MMMMMM 3",
    lab_y   = "YYYYYYY",
    coef_xm1 = "0.11*",
    coef_m1y = "0.11*",
    coef_xm2 = "0.22*",
    coef_m2y = "0.22*",
    coef_xm3 = "0.33*",
    coef_m3y = "0.33*",
    coef_xy = "0.66*"
  )


med_diagram <- function(data, height = .75, width = 2, 
                        graph_label = NA, node_text_size = 12, 
                        edge_text_size = 12, color = "black", 
                        ranksep = .2, minlen = 3){
  
  require(glue)
  require(DiagrammeR)
  
  data$height  <- height   # node height
  data$width   <- width    # node width
  data$color   <- color    # node + edge border color
  data$ranksep <- ranksep  # separation btwn mediator row and x->y row
  data$minlen  <- minlen   # minimum edge length
  
  data$node_text_size  <- node_text_size
  data$edge_text_size  <- edge_text_size
  
  data$graph_label <- ifelse(is.na(graph_label), "", 
                             paste0("label = '", 
                                    graph_label, "'"))
  
  diagram_out <- glue::glue_data(data,
                                 "digraph flowchart {
      fontname = Helvetica
      <<graph_label>>
      graph [ranksep = <<ranksep>>]

      # node definitions with substituted label text
      node [fontname = Helvetica, shape = rectangle, fixedsize = TRUE, 
      width = <<width>>, height = <<height>>, fontsize = <<node_text_size>>, 
      color = <<color>>]        
        mm1 [label = '<<lab_m1>>']
        xx [label = '<<lab_x>>']
        yy [label = '<<lab_y>>']
        mm2 [label = '<<lab_m2>>']
        mm3 [label = '<<lab_m3>>']

      # edge definitions with the node IDs
      edge [minlen = <<minlen>>, fontname = Helvetica, 
      fontsize = <<edge_text_size>>, color = <<color>>]
        xx -> yy [label = '<<coef_xy>>'];
        mm1 -> yy [label = '<<coef_m1y>>'];
        xx -> mm1 [label = '<<coef_xm1>>'];
        mm2 -> yy [label = '<<coef_m2y>>'];
        xx -> mm2 [label = '<<coef_xm2>>'];
        mm3 -> yy [label = '<<coef_m3y>>'];
        xx -> mm3 [label = '<<coef_xm3>>'];
        
      rankdir = LR;
      { rank = same; mm1; mm2; mm3 }
      
      }

      ", .open = "<<", .close = ">>")  
  
  
  DiagrammeR::grViz(diagram_out)  
}

med_diagram(med_data)

Output, Mediation Model 1:

A second version I tried, led to all mediators being in a horizontal instead of a vertical line:

med_data <-
  data.frame(
    lab_x   = "XXXXXX",
    lab_m1   = "MMMMMM 1",
    lab_m2   = "MMMMMM 2",
    lab_m3   = "MMMMMM 3",
    lab_y   = "YYYYYYY",
    coef_xm1 = "0.11*",
    coef_m1y = "0.11*",
    coef_xm2 = "0.22*",
    coef_m2y = "0.22*",
    coef_xm3 = "0.33*",
    coef_m3y = "0.33*",
    coef_xy = "0.66* (.16)"
  )


med_diagram <- function(data, height = .75, width = 2, 
                        graph_label = NA, node_text_size = 12, 
                        edge_text_size = 12, color = "black", 
                        ranksep = .2, minlen = 3){
  
  require(glue)
  require(DiagrammeR)
  
  data$height  <- height   # node height
  data$width   <- width    # node width
  data$color   <- color    # node + edge border color
  data$ranksep <- ranksep  # separation btwn mediator row and x->y row
  data$minlen  <- minlen   # minimum edge length
  
  data$node_text_size  <- node_text_size
  data$edge_text_size  <- edge_text_size
  
  data$graph_label <- ifelse(is.na(graph_label), "", 
                             paste0("label = '", 
                                    graph_label, "'"))
  
  diagram_out <- glue::glue_data(data,
                                 "digraph flowchart {
      fontname = Helvetica
      <<graph_label>>
      graph [ranksep = <<ranksep>>]

      # node definitions with substituted label text
      node [fontname = Helvetica, shape = rectangle, fixedsize = TRUE, 
      width = <<width>>, height = <<height>>, fontsize = <<node_text_size>>, 
      color = <<color>>]        
        mm1 [label = '<<lab_m1>>']
        xx [label = '<<lab_x>>']
        yy [label = '<<lab_y>>']
        mm2 [label = '<<lab_m2>>']
        mm3 [label = '<<lab_m3>>']

      # edge definitions with the node IDs
      edge [minlen = <<minlen>>, fontname = Helvetica, 
      fontsize = <<edge_text_size>>, color = <<color>>]
        xx -> yy [label = '<<coef_xy>>'];
        mm1 -> yy [label = '<<coef_m1y>>'];
        xx -> mm1 [label = '<<coef_xm1>>'];
        mm2 -> yy [label = '<<coef_m2y>>'];
        xx -> mm2 [label = '<<coef_xm2>>'];
        mm3 -> yy [label = '<<coef_m3y>>'];
        xx -> mm3 [label = '<<coef_xm3>>'];
        

      { rank = max; xx; yy}
      }

      ", .open = "<<", .close = ">>")  
  
  
  DiagrammeR::grViz(diagram_out)  
}

med_diagram(med_data)

Output, Mediation Model 2:

Help and a little input on the rank part would be amazing or an alternative package for solving this issue.

Update: Here is an example picture: Example Model

can you provide a (hand drawn) example of your desired result. — sroush, Mar 03 '23 at 21:10
@sroush sure. I updated the post and added an example picture at the end. — Coztomate, Mar 04 '23 at 11:11

sroush · Answer 1 · 2023-03-05T17:55:23.317

2

Best references for ranking: https://www.graphviz.org/pdf/dotguide.pdf (esp. p. 7 & 15) and https://www.graphviz.org/docs/attrs/rank/
All-in-all not a Graphviz strength. I do not use Diagrammer, but the Graphviz code below will probably translate pretty easily.

digraph N{
  splines=false // straight line edges
  rankdir=TB    // same as default
  nodesep=1.2
  ranksep=.2
  node [shape=rect]
 
  // set these nodes one per rank
  mm1 -> mm2 [style=invis]
  mm2 -> mm3 [style=invis]

  xxxx -> mm1:w
  xxxx -> mm2:w
  xxxx -> mm3:w
  mm1:e -> yyyy
  mm2:e -> yyyy
  mm3:e -> yyyy
  {
   rank=sink  //  rank=source   if you want these nodes on top
   // bogus node is needed to keep left-right symmetry, not sure why
   bogus [style=invis shape=plain]
   xxxx -> yyyy
   xxxx -> bogus [style=invis]
   bogus -> yyyy [style=invis]
  }
}

Giving:

edited Mar 05 '23 at 17:55

answered Mar 04 '23 at 22:57

sroush

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That looks great. Unfortunately, once I add labels to the edges they are getting bent. It's either curved with `splines=true`or bent with `splines=false`. There seems to be no way to force the line to stay straight. I tried adding labels like: `xxxx -> mm1:w [label = 'label xm1'] xxxx -> mm2:w [label = 'label xm2'] xxxx -> mm3:w [label = 'label xm3'] mm1:e -> yyyy [label = 'label m1y'] mm2:e -> yyyy [label = 'label m2y'] mm3:e -> yyyy [label = 'label m2y']` – Coztomate Mar 06 '23 at 09:37
If you use **xlabel** instead of **label**, the edges will remain straight. You may also want to tweak **nodesep** and **ranksep** – sroush Mar 06 '23 at 15:07
That worked. The edges are straight. Unfortunately, the labels of the edges are overlapping with the edges making them barely readable. I checked several threads about this here. There seems to be no good solution. I tried with headlabel and taillabel and labeldistance but this just makes it look weird. – Coztomate Mar 08 '23 at 15:04
Try adding spaces or newlines (\n) before and/or after the text of the labels. – sroush Mar 08 '23 at 17:17
Tried that. Unfortunately, the result varies a lot and is unpredictable. Maybe I just add the labels by hand afterward. Thanks. – Coztomate Mar 09 '23 at 13:03
you can explicitly reposition labels like this: dot -Tdot myfile.gv>myfile.dot; then edit myfile.dot w/ favorite editor, modify **lp** or **xlp** values; then neato -n2 -Tpng myfile.dot >myfile.png – sroush Mar 09 '23 at 15:48
You can often move labels by adding extra spaces to the text: xlabel=" my label" or label="my label " – sroush Apr 07 '23 at 23:45

Drawing diagram of a multiple / parallel mediation model in R

1 Answers1