semPaths() prints plot even when plot is assigned to an object

[fschaffner]

Hi @SachaEpskamp, thanks for creating and maintaining this package!

I noticed that semPaths() prints the figure to the viewer even when the plot is assigned to an object, which is generally not how we would expect R functions to work. When a function is called without assigning to an object, we expect the result to be printed in the console, e.g., lm(wt ~ cyl, data = mtcars). But if we assign it to an object we don't expect the result to be printed in the console, e.g., model <- lm(wt ~ cyl, data = mtcars). This is especially problematic when using Rmarkdown, because when I assign the plot to an object, the figure still appears in the knitted HTML document, even though it shouldn't. Can this be changed?

(The reason I am asking is that I assign the figure to an object that I then post-process using other packages like semptools, and I don't want the figure to appear multiple times in my knitted Rmarkdown document.)

Rscript example: Note that the plot shouldn't be printed because I am assigning it to an object!

library("lavaan")
#> This is lavaan 0.6-10
library("semPlot")

# A silly dataset:
X <- rnorm(100)
Y <- rnorm(100)
Z <- rnorm(1) * X + rnorm(1) * Y + rnorm(1) * X * Y
DF <- data.frame(X, Y, Z)

# Regression including interaction:
res <- lm(Z ~ X * Y, data = DF)

# Path diagram:
plot <- semPaths(res) # => The figure shouldn't be printed

^{Created on 2022-03-04 by the reprex package (v2.0.1)}

Session info

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#> #> ────────────────────────────────────────────────────────────────────────────── ```

Rmarkdown example

---
title: "Reproducible Example"
output: html_document
---

```{r}
library("lavaan")
library("semPlot")

# A silly dataset:
X <- rnorm(100)
Y <- rnorm(100)
Z <- rnorm(1) * X + rnorm(1) * Y + rnorm(1) * X * Y
DF <- data.frame(X, Y, Z)

# Regression including interaction:
res <- lm(Z ~ X * Y, data = DF) 

# Path diagram:
plot <- semPaths(res) # => The figure shouldn't be printed

[sfcheung]

I am not a developer of semPlot (I love using it and use it a lot in my teaching; thanks, @SachaEpskamp, for developing this package). I just want to share how I solve this problem. There may be a better solution.

You can set DoNotPlot = TRUE when calling semPlot::semPaths(). This will suppress the plot in Rmarkdown.

This is an example

---
title       : "Demo: DoNotPlot"
---

# Diagram not plotted

```{r}
library(semPlot)
X <- rnorm(100)
Y <- rnorm(100)
Z <- rnorm(1)*X + rnorm(1)*Y + rnorm(1)*X*Y
DF <- data.frame(X,Y,Z)
res <- lm(Z ~ X*Y, data = DF)
p <- semPaths(res,"est","hide", intAtSide=TRUE,
              DoNotPlot = TRUE)

Diagram plotted

plot(p)

[SachaEpskamp]

Hi both,

Yes indeed the argument DoNotPlot is designed for this, thank you Shu Fai!

I think it is pretty common for base R graphics to create a plot even when the result is stored in an object. For example, all these commands to that:

object <- plot(rnorm(100),rnorm(100))
object <- hist(rnorm(100))
object <- pairs(matrix(rnorm(400),100,4))

Best, sacha

[fschaffner]

Thanks for the explanations @sfcheung and @SachaEpskamp!