Opacity of split compound nodes is 0.6 for the split part

[micwij]

Hi,

I tried SBGN View with a minimal custom SBGN, to see if I can manage to visualize omics data of both transcriptome and metabolome via SBGN_View. I noticed that if compound nodes are split, the right part has only an opacity/alpha of 0.6 when opening the .svg in inkscape. First I thought this may be due to my SBGN-file, but the same happens, when using the example in 5.2 of the vignette (https://bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/SBGNview.Vignette.html#53_Visualize_both_gene_data_and_compound_data). It would be great if you could check this.

Best,
Micha

[micwij]

I think I found the setting in "plot.utilities.R":
In the functions plot.path() and plot.rectangle() there are the arguments "fill.opacity = 0.6" (line 281 and 331) and in line 2700 "fill.opacity = 0.8". At least for the first two, I think it should be 1 otherwise it affects the omics mapping. Do you agree or am I overlooking some reason, why this should not be 1?

I may try to fork this and submit a pull request (I am fairly new to working with GitHub).

[raw937]

Are you still having this issue? Let me know?

This project is no longer under development here.
Please check the new fork here.
https://github.com/Kannapolis-Bioinformatics/SBGNview

If you have the same issues place in https://github.com/Kannapolis-Bioinformatics/SBGNview/issues.

many thanks,
Rick