Can not render .pdf file format

[alireza5969]

I am using {ggplot} and {marquee} to render a plot. I tried to save the plot in .pdf format but somehow the file I got is broken.

For example, this is what I get when I open it on a Windows machine using Adobe Reader:

I tried to:

1. open the file on an Android device:
2. render the plot in .png which works as I expected:
   

FYI this is my code:

range_max_dum <- 0.015
point_size <- 3
gray_line_size <- point_size - .75
max_color <- "#176b87"
min_color <- "#ffab40"

dum_legend <- glue::glue(
"Pooled effect sizes from {.[max_color] **all the included studies**} and {.[min_color] **when outliers and < median samle sizes removed**}", 
.open = "[",
.close = "]")

dum_plot_data <- 
    tibble::tribble(
        ~country,       ~es.x,       ~ul.x,       ~ll.x,       ~es.y,       ~ul.y,       ~ll.y,     ~min_es,
        "China", 0.035799021, 0.044116242,  0.02832098, 0.023210599, 0.029256901, 0.017848775, 0.017848775,
        "United Kingdom", 0.011771449, 0.032197434, 0.001366486, 0.004588374, 0.008391918, 0.001920112, 0.001366486,
        "United Arab Emirates", 0.010544074, 0.013057569, 0.008294895, 0.010544074, 0.013057569, 0.008294895, 0.008294895,
        "India", 0.050080298,  0.07488636, 0.030041038, 0.019575116, 0.037859183, 0.007191735, 0.007191735,
        "Saudi Arabia", 0.003460838, 0.004283512, 0.002725023, 0.003460838, 0.004283512, 0.002725023, 0.002725023,
        "Canada", 0.024949252, 0.038100772,  0.01451395, 0.011457303,  0.01343168, 0.009637608, 0.009637608
    )
  
dum_plot_data %>% 
  ggplot(aes(y = country)) +
  
  geom_linerange(
    aes(xmin = es.y, xmax = es.x), 
    color = "gray65", 
    linewidth = gray_line_size,
    alpha = .32) +
  
  geom_linerange(
    xmin = -.05, 
    aes(xmax = min_es), 
    color = "gray10", 
    linetype = 5,
    linewidth = .35,
    alpha = .45) +
  
  geom_point(
    aes(x = es.y), 
    color = min_color, 
    size = point_size) +
  
  geom_linerange(
    aes(xmin = ll.y, xmax = ul.y),
    color = min_color,
    alpha = .5) +
  
  geom_point(
    aes(x = es.x), 
    color = max_color, 
    size = point_size) + 
  
  geom_linerange(
    aes(xmin = ll.x, xmax = ul.x),
    color = max_color,
    alpha = .5) +
  
  scale_x_continuous(
    limits = c(0, range_max_dum), labels = scales::label_percent(), 
    breaks = seq(0, range_max_dum, by = .05)) + 
  
  labs(
    x = "Incidence",
    title = dum_legend) +
  
  theme_minimal() +
  
  theme(
    panel.grid.major.y = element_blank(), 
    panel.grid.minor.y = element_blank(),
    panel.grid.minor.x = element_blank(), 
    axis.title.y = element_blank(), 
    axis.title.x = element_text(face = "bold", size = 12.5),
    axis.text.x = element_text(hjust = 1, size = 10), 
    plot.title = element_marquee(width = 1))

ggsave(
  filename = "test.pdf", 
  device = "pdf",
  width  =  20,
  height =  30,
  units  = "cm")

Session Info:

sessionInfo()

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Asia/Tehran
tzcode source: internal

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

other attached packages:
 [1] marquee_0.1.0                
 [2] ggtext_0.1.2                 
 [3] glue_1.7.0                   
 [4] ggforce_0.5.0                
 [5] showtext_0.9-6               
 [6] showtextdb_3.0               
 [7] sysfonts_0.8.8               
 [8] sf_1.0-16                    
 [9] rnaturalearthhires_1.0.0.9000
[10] rnaturalearthdata_1.0.0      
[11] rnaturalearth_1.0.1          
[12] furrr_0.3.1.9000             
[13] future_1.34.0                
[14] magick_2.8.3                 
[15] officer_0.6.7                
[16] flextable_0.9.7              
[17] broom_1.0.6                  
[18] metafor_4.6-0                
[19] numDeriv_2016.8-1.1          
[20] metadat_1.2-0                
[21] Matrix_1.6-5                 
[22] janitor_2.2.0                
[23] lubridate_1.9.3              
[24] forcats_1.0.0                
[25] stringr_1.5.1                
[26] dplyr_1.1.4                  
[27] purrr_1.0.2                  
[28] readr_2.1.5                  
[29] tidyr_1.3.1                  
[30] tibble_3.2.1                 
[31] ggplot2_3.5.1                
[32] tidyverse_2.0.0              

loaded via a namespace (and not attached):
 [1] DBI_1.2.1              
 [2] readxl_1.4.3           
 [3] rlang_1.1.4            
 [4] magrittr_2.0.3         
 [5] snakecase_0.11.1       
 [6] e1071_1.7-14           
 [7] compiler_4.3.3         
 [8] systemfonts_1.1.0      
 [9] vctrs_0.6.5            
[10] pkgconfig_2.0.3        
[11] crayon_1.5.3           
[12] fastmap_1.2.0          
[13] backports_1.4.1        
[14] labeling_0.4.3         
[15] utf8_1.2.4             
[16] rmarkdown_2.29         
[17] tzdb_0.4.0             
[18] camcorder_0.1.0        
[19] ragg_1.3.3             
[20] xfun_0.49              
[21] jsonlite_1.8.9         
[22] tweenr_2.0.2           
[23] uuid_1.2-1             
[24] terra_1.7-71           
[25] parallel_4.3.3         
[26] R6_2.5.1               
[27] stringi_1.8.3          
[28] parallelly_1.39.0      
[29] car_3.1-2              
[30] cellranger_1.1.0       
[31] Rcpp_1.0.13-1          
[32] knitr_1.49             
[33] timechange_0.3.0       
[34] tidyselect_1.2.1       
[35] rstudioapi_0.16.0      
[36] abind_1.4-8            
[37] codetools_0.2-19       
[38] listenv_0.9.1          
[39] lattice_0.22-5         
[40] withr_3.0.2            
[41] askpass_1.2.1          
[42] evaluate_1.0.1         
[43] units_0.8-5            
[44] proxy_0.4-27           
[45] polyclip_1.10-6        
[46] zip_2.3.1              
[47] xml2_1.3.6             
[48] pillar_1.9.0           
[49] carData_3.0-5          
[50] KernSmooth_2.23-22     
[51] generics_0.1.3         
[52] rprojroot_2.0.4        
[53] mathjaxr_1.6-0         
[54] hms_1.1.3              
[55] munsell_0.5.1          
[56] scales_1.3.0           
[57] globals_0.16.3         
[58] class_7.3-22           
[59] gdtools_0.4.1          
[60] tools_4.3.3            
[61] data.table_1.16.2      
[62] grid_4.3.3             
[63] colorspace_2.1-1       
[64] nlme_3.1-164           
[65] cli_3.6.3              
[66] textshaping_0.4.0      
[67] rsvg_2.6.0             
[68] fontBitstreamVera_0.1.1
[69] fansi_1.0.6            
[70] svglite_2.1.3          
[71] gtable_0.3.6           
[72] rstatix_0.7.2          
[73] digest_0.6.36          
[74] fontquiver_0.2.1       
[75] classInt_0.4-10        
[76] gifski_1.12.0-2        
[77] farver_2.1.2           
[78] htmltools_0.5.8.1      
[79] lifecycle_1.0.4        
[80] here_1.0.1             
[81] httr_1.4.7             
[82] gridtext_0.1.5         
[83] fontLiberation_0.1.0   
[84] openssl_2.2.2          
[85] MASS_7.3-60.0.1        

[thomasp85]

@pmur002 this would appear to be a bug in the implementation of glyph support in pdf? Can you see if that is the case?

[alireza5969]

I asked around on StackOverflow here. It seems that the code works fine on Mac but the issue is reproducible on Windows.

[pmur002]

Try using the grDevices::embedGlyphs() function to embed the font within the pdf document.

This is (very) briefly mentioned here: https://www.stat.auckland.ac.nz/~paul/Reports/Typography/glyphs/glyphs.html