Error in grid.Call(C_stringMetric, as.graphicsAnnot(x$label))

Question

[yueli7]

Hello,

I tired to use ggplot.

I think there is something wrong with the font, but I have no idea.

Thank you in advance for great help!

Best,

Yue

> pep_plot <- ggplot(peptide_summary,
+        aes(x = start, xend = end, y = spectral_count, yend = spectral_count)) +
+   geom_segment(size = 1) +
+   ylim(0, 5) + 
+   xlab("peptide position within protein") +
+   ylab("peptide count")

> pep_plot
Error in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) : 
X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 11 could not be loaded


> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] shiny_1.5.0    extrafont_0.17 dplyr_0.8.2    ggplot2_3.3.2  parsemsf_0.1.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5       later_1.1.0.1    pillar_1.4.7     compiler_3.6.1  
 [5] dbplyr_1.3.0     highr_0.8        tools_3.6.1      digest_0.6.27   
 [9] bit_4.0.4        RSQLite_2.2.1    memoise_1.1.0    lifecycle_0.2.0 
[13] tibble_3.0.4     gtable_0.3.0     pkgconfig_2.0.3  rlang_0.4.9     
[17] DBI_1.1.0        xfun_0.19        fastmap_1.0.1    Rttf2pt1_1.3.8  
[21] withr_2.3.0      stringr_1.4.0    knitr_1.30       vctrs_0.3.5     
[25] bit64_4.0.5      grid_3.6.1       tidyselect_1.1.0 glue_1.4.2      
[29] R6_2.5.0         tidyr_1.1.2      purrr_0.3.4      farver_2.0.3    
[33] extrafontdb_1.0  blob_1.2.1       magrittr_2.0.1   promises_1.1.1  
[37] htmltools_0.5.0  scales_1.1.1     ellipsis_0.3.1   assertthat_0.2.1
[41] xtable_1.8-4     mime_0.9         colorspace_2.0-0 httpuv_1.5.4    
[45] labeling_0.4.2   stringi_1.5.3    lazyeval_0.2.2   munsell_0.5.0   
[49] crayon_1.3.4

[Ram]

Try using ggsave to write the plot to a file and then opening that file. This could be a problem with the graphical display device.

[yueli7]

Hello _r_am,

Thank you so much for your great help!

Thank you again and really apprectiated!

Best,

Yue

I tried to use ggsave to save the plot.

> pep_plot <- ggplot(peptide_summary,
+        aes(x = start, xend = end, y = spectral_count, yend = spectral_count)) +
+   geom_segment(size = 1) +
+   ylim(0, 5) + 
+   xlab("peptide position within protein") +
+   ylab("peptide count")

 > ggplot2::ggsave(filename="protein", plot=pep_plot, device="eps",dpi=1200, width=15, height=10, units="cm")

[Ram]

I tried to use ggsave to save the plot

And what happened? Why use an eps device instead of, say, png or pdf?

[yueli7]

Hello _r_am,

Thank yo so much for your comments!

Thank you again!

Best,

Yue

> ggplot2::ggsave(filename="protein.pdf", plot=pep_plot)
Saving 7 x 7 in image

> ggplot2::ggsave(filename="protein.png", plot=pep_plot)
Saving 7 x 7 in image

[Ram]

Please don't ask to be spoonfed each step. Just let us know if it worked or not.