Hello,

I am using the STRINGdb R package and use the plot_network command to generate a network graphic and save it to a

PDF file:

  string_db <- STRINGdb$new( version="10", species=9606, score_threshold=400, input_directory=getwd() )

  pdf(file.path(outDir, network_file_name), width=14)
    string_db$plot_network( hits )
  dev.off()

The network is generated fine. However the link to string-db.org which is inserted below the network (and which is very useful) is not working. Having had a closer look at it, I found out that the dash character '-' was actually not a dash but a special character that caused the URL to fail.

I was wondering if that is a known issue on some platforms...

Below is the output of my sessionInfo.

Thanks for your help!

Florian

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
[1] C

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

other attached packages:
[1] cogena_1.8.0    kohonen_2.0.19  MASS_7.3-44     class_7.3-14
[5] ggplot2_2.2.0   cluster_2.0.5   STRINGdb_1.14.0

loaded via a namespace (and not attached):
 [1] fastcluster_1.1.21  gtools_3.5.0        corrplot_0.77
 [4] reshape2_1.4.2      lattice_0.20-34     pcaPP_1.9-61
 [7] colorspace_1.3-1    amap_0.8-14         stats4_3.3.2
[10] hash_2.2.6          chron_2.3-47        withr_1.0.2
[13] DBI_0.5-1           BiocGenerics_0.20.0 RColorBrewer_1.1-2
[16] biwt_1.0            gsubfn_0.6-6        foreach_1.4.3
[19] plyr_1.8.4          stringr_1.1.0       robustbase_0.92-6
[22] munsell_0.4.3       gtable_0.2.0        caTools_1.17.1
[25] devtools_1.12.0     mvtnorm_1.0-5       codetools_0.2-15
[28] memoise_1.0.0       Biobase_2.34.0      doParallel_1.0.10
[31] parallel_3.3.2      DEoptimR_1.0-8      proto_1.0.0
[34] Rcpp_0.12.8         KernSmooth_2.23-15  scales_0.4.1
[37] gdata_2.17.0        plotrix_3.6-3       apcluster_1.4.3
[40] gplots_3.0.1        png_0.1-7           digest_0.6.10
[43] stringi_1.1.2       dplyr_0.5.0         grid_3.3.2
[46] tools_3.3.2         bitops_1.0-6        magrittr_1.5
[49] sqldf_0.4-10        lazyeval_0.2.0      RCurl_1.95-4.8
[52] tibble_1.2          RSQLite_1.0.0       rrcov_1.4-3
[55] Matrix_1.2-7.1      assertthat_0.1      iterators_1.0.8
[58] mclust_5.2          R6_2.2.0            igraph_1.0.1

Hello Florian,

i think the pdf device in R is having a hard time encoding some characters, so the easiest solution is to simply use the cairo_pdf instead of the pdf, e.g.:

cairo_pdf(file.path(outDir, network_file_name), width=14)

We could create a separate function in STRINGdb in the future (something like savePDF) that would automatically use cairo_pdf.

Hope this helps,
Gregor

Thanks! That worked.
I am surprised that the default pdf device has issues with a simple dash, but I am not an R person and as long as I can get my script working I am happy.

Thanks!

Florian