Drawing simple mediation diagram in R

You can use the 'psych' package to test your moderation/mediation and it will give you a plot as well.

mediate(Output ~ Independent1 + (Mediator), data =mydata)

Here are two versions of a mediation diagram built with DiagrammeR and a third built with TikZ. Each has strengths and weaknesses:

• DiagrammeR + Graphviz:

  • Pros: easy to create diagrams with provided function, lots of options to adjust design of nodes.
  • Cons: few options to adjust text on edges, output is an htmlwidget object that can print to pdf but may require conversion under specific circumstances such as within a for-loop.

• TikZ

  • Pros: highly customizable, including text on edges; easy to generate diagram with provided function
  • Cons: if you need HTML output, it's designed for LaTeX; syntax can be confusing

• DiagrammeR native syntax (offered just for completeness)

  • Pros: code very easy to read, edit for R users
  • Cons: even fewer apparent ways to adjust text on edges

I've coded the first and second examples with a function med_diagram that uses the glue package to assemble the relevant graphviz or TikZ code. The function requires a data.frame that expects one row with columns for relevant labels and coefficients. For the DiagrammeR-specific function, there are also arguments to adjust various elements of the design.

Diagrammer + Graphviz

med_data <-
  data.frame(
    lab_x   = "Math\\nAbility",
    lab_m   = "Math\\nself-efficacy",
    lab_y   = "Interest in the\\nmath major",
    coef_xm = ".47*",
    coef_my = ".36*",
    coef_xy = "0.33* (.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>>]        
        mm [label = '<<lab_m>>']
        xx [label = '<<lab_x>>']
        yy [label = '<<lab_y>>']

      # edge definitions with the node IDs
      edge [minlen = <<minlen>>, fontname = Helvetica, fontsize = <<edge_text_size>>, color = <<color>>]
        mm -> yy [label = '<<coef_my>>'];
        xx -> mm [label = '<<coef_xm>>'];
        xx -> yy [label = '<<coef_xy>>'];
      
      { rank = same; mm }
      { rank = same; xx; yy }
      
      }

      ", .open = "<<", .close = ">>")  


DiagrammeR::grViz(diagram_out)  
}

med_diagram(med_data)

TikZ

TikZ and PGF need to be loaded as LaTeX packages in the preamble. The sample code below includes both those packages and some additional commands that, for example, set a global specification for 'mynode' used in the diagram. I received a warning to include \pgfplotsset{compat=1.17} in my preamble but that may not be necessary for others. Note, this code builds on the example provided here: https://tex.stackexchange.com/a/225940/34597

---
title: "Sample Rmd"
author: "Your name here"
output: pdf_document
header-includes:
  - \usepackage{tikz}
  - \usepackage{pgfplots}
  - \pgfplotsset{compat=1.17}
  - \tikzset{mynode/.style={draw,text width=1in,align=center} }
  - \usetikzlibrary{positioning}
---

```{r, load_packages, include = FALSE}
library(glue)
```
  
```{r, load_function}
med_diagram_tikz <- function(data) {
  glue::glue_data(med_data, 
"
\\begin{figure}
\\begin{center}
\\begin{tikzpicture}[font=\\sffamily]
    \\node[mynode] (m){<<lab_m>>};
    \\node[mynode,below left=of m](x) {<<lab_x>>};
    \\node[mynode,below right=of m](y) {<<lab_y>>};
    \\draw[-latex] (x.north) -- node[auto] {<<coef_xm>>} (m.west);
    \\draw[-latex] (m.east) -- node[auto] {<<coef_my>>} (y.north);
    \\draw[-latex] (x.east) --
            node[below=2mm, align=center] {<<coef_xy>>} (y.west);
\\end{tikzpicture}
\\end{center}
\\end{figure}
", 
.open = "<<", .close = ">>"
)
}
```
  
  
```{r create_diagram, echo = FALSE, results = 'asis'}
med_data <-
  data.frame(
    lab_x   = "Math\\\\Ability",
    lab_m   = "Math\\\\self-efficacy",
    lab_y   = "Interest in the\\\\math major",
    coef_xm = ".47*",
    coef_my = ".36*",
    coef_xy = "0.33* (.16)"
  )

tikz_diagram_out <- med_diagram_tikz(med_data)

# requires chunk header to be set to results = 'asis'
cat("\n", tikz_diagram_out, "\n")

```

Diagrammer native syntax

This third version of a mediation diagram uses syntax that's more easily understood by R users but I don't love how the edge label text gets placed oddly (hence the two alternative versions above).

library(DiagrammeR)

# Create a node data frame (ndf)
ndf <- create_node_df(
  n         = 3,
  label     = c( "Math\nself-efficacy","Math\nability", "Interest in\nthe math major"),
  shape     = rep("rectangle", 3),
  style     = "empty",
  fontsize  = 6,
  fixedsize = TRUE,
  height    = .5,
  width     = .75,
  color     = "gray80",
  x         = c(1, 2, 3),
  y         = c(1, 2, 1)
)

# Create an edge data frame (edf)
edf <- create_edge_df(
  from     = c(1, 1, 2),
  to       = c(2, 3, 3),
  label    = c(".47*", ".33* (.16)", ".36*"),
  fontsize = 6,
  minlen   = 1,
  color    = "gray80",
  )

# Create a graph with the ndf and edf
graph <- create_graph(
  nodes_df = ndf,
  edges_df = edf
  )

graph %>%
  render_graph()

While @baptiste solution might work as well, I was looking for a publishable format.

Function plotmat from library(diagram) is the one that got me the closest to my example:

For a reproducible example use:

library(diagram)
data <- c(0, "'.47*'", 0,
          0, 0, 0, 
          "'.36*'", "'.33* (.16)'", 0)
M<- matrix (nrow=3, ncol=3, byrow = TRUE, data=data)
plot<- plotmat (M, pos=c(1,2), 
                name= c( "Math self-efficacy","Math ability", "Interest in the math major"), 
                box.type = "rect", box.size = 0.12, box.prop=0.5,  curve=0)