string-db.org link not working in generated graphic
2
0
Entering edit mode
@florianreisinger-11918
Last seen 4.8 years ago

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

 

STRINGdb • 744 views
ADD COMMENT
1
Entering edit mode
Gregor Rot ▴ 10
@gregor-rot-11919
Last seen 4.2 years ago
Zurich, Switzerland

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

ADD COMMENT
0
Entering edit mode
@florianreisinger-11918
Last seen 4.8 years ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 247 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6