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rggplot2pdfr-markdownggraph

Error in grid.Call.graphics while knitting Rmarkdown

I try to knit my Rmarkdown-file to a pdf-document. I get the following error:

Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
invalid character set type

This is the code I used:

comparison <- layout_with_fr(graph)

tidyclassroom <- as_tbl_graph(graph)

tidyclassroom %>%
  activate("nodes") %>%
  ggraph(layout=comparison) +
  geom_edge_link(
    end_cap = circle(12, "pt"),
    color = "grey", 
    arrow = arrow(length=unit(5, "pt"))) +
  geom_node_point(size=10, shape=21, fill=ifelse(V(graph)$sex == 2, "pink", "lightblue")) +
  geom_node_text(aes(label = name), colour = 'black', vjust = 0.4) +
  ggtitle('August 2023') +
  theme_graph() +
  theme(plot.title = element_text(hjust = 0.5))

For further explanation: I used an object called "comparison" because I have another network for another time point.

The code works when I don't use it in Rmarkdown. It also works as HTML (although I get some warning messages that I ignored).

I have read that it has something to do with the font type but I don't know how to solve this problem because I did not set the font size manually.

Solution

  • As you and @Julian already noted, this looks like a font issue. And the issue is that ggraph::theme_graph() uses "Arial Narrow" by default and which besides the error throws the following warnings:

    In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : font family 'Arial Narrow' not found in PostScript font database

    One option to fix that is to use e.g. the default "sans" font by setting base_family = "sans".

    Using the default example from ggraph:

    ---
title: "Untitled"
output: pdf_document
date: "2024-08-24"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```

```{r}
library(ggraph)
library(tidygraph)

# Create graph of highschool friendships
graph <- as_tbl_graph(highschool) |>
  mutate(Popularity = centrality_degree(mode = "in"))

# plot using ggraph
ggraph(graph, layout = "kk") +
  geom_edge_fan(aes(alpha = after_stat(index)), show.legend = FALSE) +
  geom_node_point(aes(size = Popularity)) +
  facet_edges(~year) +
  theme_graph(
    base_family = "sans",
    foreground = "steelblue", fg_text_colour = "white"
  )
```

    enter image description here

    A second option which also worked fine for me is to use "cairo_pdf" as the plotting device (which also worked for me even if the font is not available, e.g. I tested with base_family = "foobarbaz") which could be set using

    ```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, dev="cairo_pdf")
```

    And a third option which also worked fine for me (but requires that the font is available) is to use the extrafont package as suggested in the R Graphics Cookbook.