ggsave pdf issue

[PCEBrunaLab]

Trying to save a PDF of a plot. Saves fine as a PNG but for some reason most of the plot is missing as a PDF (plots attached).
Run on two different R servers, same issue.
clone_distribution_filtered_cut_bg.pdf

Can send data for plotting if helpful.

> filt3a.gg + filt3b.gg + filt3c.gg +
+   plot_layout(axis_titles = "collect") &
+   theme(axis.ticks.x = element_blank(),
+         plot.background = element_rect(fill = "transparent", color = NA),
+         text = element_text(20))
> ggsave("clone_distribution_filtered_cut_bg.pdf", width = 16.5, height = 5.8, bg = "transparent")
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
2: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
3: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
4: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
5: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
6: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
7: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
8: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
9: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
10: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
11: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
12: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
13: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
14: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
15: In grid.Call(C_textBounds, as.graphicsAnnot(x$label),  ... :
  font family '20' not found in PostScript font database
16: In grid.Call(C_textBounds, as.graphicsAnnot(x$label),  ... :
  font family '20' not found in PostScript font database
17: In grid.Call(C_textBounds, as.graphicsAnnot(x$label),  ... :
  font family '20' not found in PostScript font database
18: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
19: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
20: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
21: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
22: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
23: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
24: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
25: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
26: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
27: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
28: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
29: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
30: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
31: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
32: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
33: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
34: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
35: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
36: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
37: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
38: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
39: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
40: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
41: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
42: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
43: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
44: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
45: In grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  font family '20' not found in PostScript font database
46: In grid.Call(C_textBounds, as.graphicsAnnot(x$label),  ... :
  font family '20' not found in PostScript font database
47: In grid.Call(C_textBounds, as.graphicsAnnot(x$label),  ... :
  font family '20' not found in PostScript font database
48: In grid.Call(C_textBounds, as.graphicsAnnot(x$label),  ... :
  font family '20' not found in PostScript font database
49: In grid.Call(C_textBounds, as.graphicsAnnot(x$label),  ... :
  font family '20' not found in PostScript font database
50: In grid.Call(C_textBounds, as.graphicsAnnot(x$label),  ... :
  font family '20' not found in PostScript font database

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Rocky Linux 8.9 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so;  LAPACK version 3.9.0

locale:
[1] C

time zone: UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] patchwork_1.2.0.9000 lubridate_1.9.3      forcats_1.0.0        stringr_1.5.1       
 [5] dplyr_1.1.3          purrr_1.0.2          readr_2.1.5          tidyr_1.3.1         
 [9] tibble_3.2.1         ggplot2_3.5.1        tidyverse_2.0.0     

loaded via a namespace (and not attached):
 [1] gtable_0.3.4      compiler_4.3.2    crayon_1.5.2      tidyselect_1.2.1  textshaping_0.3.7
 [6] systemfonts_1.0.6 scales_1.3.0      R6_2.5.1          labeling_0.4.3    generics_0.1.3   
[11] munsell_0.5.0     pillar_1.9.0      tzdb_0.4.0        rlang_1.1.3       utf8_1.2.4       
[16] stringi_1.8.3     timechange_0.3.0  cli_3.6.2         withr_3.0.0       magrittr_2.0.3   
[21] grid_4.3.2        rstudioapi_0.16.0 hms_1.1.3         lifecycle_1.0.4   vctrs_0.6.5      
[26] glue_1.7.0        farver_2.1.1      ragg_1.2.7        fansi_1.0.6       colorspace_2.1-0 
[31] tool

[teunbrand]

This is probably due to using a custom font that isn't included in the example. A more minima and complete reprex below, that mirrors the error messages and missing annotations in the plot.

library(ggplot2)

p <- ggplot(mpg, aes(displ, hwy)) +
  geom_point() +
  theme(text = element_text("Impact"))

ggsave("test.pdf", p)

This isn't an issue with ggplot2 but between {grid} and the graphics device, so I'll close this here. You can try the {extrafont} approach described here: https://r-graphics.org/recipe-output-fonts-pdf.