Tool:SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species

Question

[bigmawen]

Dear all,

The new SBGNview package has been released with major updates and improvement:

GitHub: https://github.com/datapplab/SBGNview

BioC: https://bioconductor.org/packages/SBGNview/

SBGNview is a tool set for pathway based data visualization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview package, with the following key features:

• Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN);
• Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc) and user defined pathways;
• Covers 5,200 reference pathways and over 3,000 species by default;
• Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight;
• SBGN pathway data manipulation, processing, extraction and analysis.

You may find an overview and quick start examples here: https://github.com/datapplab/SBGNview

Main tutorial: https://bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/SBGNview.Vignette.html

Analysis workflow: https://bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/pathway.enrichment.analysis.html

Please try it out and let us know if you have any comments/suggestions. Thank you!

[greyman]

Hi, I have tried the package, it was pretty great although there are some mistakes in the Rcode (vignette). I have write an email to inform the author. I wonder if you can tell me why the expression of some metabolites (circles) has only been painted half (half blue and half grey) while some others are entirely blue/yellow ? I couldn't find an explanation in the manual and the vignette, considering I only focus on one sample on my metabolomics data (only one expression column).

[bigmawen]

Greyman,
Thanks for reporting the issue. As mentioned in the post, we just made some major updates recently. It is likely you are using some old version. You would need to install the latest versions of both SBGNview.data and SBGNview packages.

In both Pathview and SBGNview, gene nodes (rectangles) and compound nodes are divided into multiple slices corresponding to the number of samples/experiments/columns in your input data. if you have a single column matrix or vector as input data, we will only see one color piece. we will add some description on this to help first-time users. Thanks.

[greyman]

bigmawen,

thank you for the reply. I wondered if multiple kegg compound accession id point to the same metabolites circle. Attached is the output that confused me, as i can see for "Ca2+", half of it is dark blue while another half is light blue, since I only have one vector.

[greyman]

hi,

thank you very much for the fast response, it is the issue of my bioconductor and the package has worked smoothly for me now. However, I am wondering why some pathways do not show up in the search eventhough it is a pathway that can be found in hsa? And how to do a species specific pathway search in the package? I am interested to look at "Dorso-ventral axis formation" of drosophila (dme) which can be found in kegg ortholog database, it does not show up when i use findPathwyas() to look for it, did I miss out some steps at this point? I tried to customized the sbgn-ml file with kegg translator, yet my input shows an error:

SBGNview(gene.data = gene.data, input.sbgn = "../Downloads/ko04320-ortholog.sbgn", output.file = "dorso_output", gene.id.type = "KO", output.formats = c("png","pdf"))

Processing pathway: ../Downloads/ko04320-ortholog.sbgn

../Downloads/ko04320-ortholog.sbgn looks like a local file. Using it directly.

Using user defined pathway SBGN-ML file!!

Error in parse.omics.data(gene.data, cpd.data, input.sbgn.full.path, database, : Must provide 'sbgn.gene.id.type'!

I included the sbgn.gene.id.type with "ko" this time:

dorso.test <- SBGNview(gene.data = gene.data, input.sbgn = "../Downloads/ko04320-ortholog.sbgn", output.file = "dorso_output", sbgn.gene.id.type = "KO", gene.id.type = "KO", max.gene.value = 0.01, min.gene.value = -0.01, output.formats = c("png","pdf"))

Processing pathway: ../Downloads/ko04320-ortholog-test.sbgn

../Downloads/ko04320-ortholog-test.sbgn looks like a local file. Using it directly.

Using user defined pathway SBGN-ML file!!

reading SBGN-ML file for arcs info: .//../Downloads/ko04320-ortholog-test.sbgn Rendering SBGN graph checking graph size and create margin for color panel parsing ports parsing glyphs

Map language is hybrid any

parsing arcs [1] "using original edges" plotting color panel SBGNview object generated

dorso.test

cannot open file 'dorso_output_../Downloads/ko04320-ortholog.sbgn.svg': No such file or directoryError in file(file, >ifelse(append, "a", "w")) : cannot open the connection

Is there a way to link this package to the kegg pathway database? Above is the SBGN file, do i need to customize another file to get it works? If so, can you give me some suggestion or to include this in the future R tutorial?

[kvegesna]

Hello greyman,

When passing a SBGN file to SBGNview function, the input.sbgn argument takes the name of the file ("ko04320-ortholog.sbgn"). If the file you are using is in a different directory, you need to specify the path to the directory containing the SBGN file using the sbgn.dir argument. Also, make sure you specify the org argument in SBGNview function (org = "dme").

Your code should look something like this:

dorso.test <- SBGNview(gene.data = gene.data, org = "dme", input.sbgn = "ko04320-ortholog.sbgn", sbgn.dir = "../Downloads",output.file = "dorso_output", sbgn.gene.id.type = "KO", gene.id.type = "KO", max.gene.value = 0.01,min.gene.value = -0.01, output.formats = c("png","pdf"))

[greyman]

Thank you, I will open a new thread to post the mapping issue,

Map language is NA

Error in if (map.language == "entity relationship") { : missing value where TRUE/FALSE needed

[greyman]

Hi, below is the post of question, I hope this is the final hurdle, thank you very much!

How to make SBGNview accepts custom sbgn input or kegg pathway? ID mapping tables between gene IDs and SBGN file glyph IDs.

[bigmawen]

greyman,
SBGNview covers major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP etc) and custom pathways in SBGN format.
https://github.com/datapplab/SBGNview

we’ve developed another package Pathview, which focuses on KEGG pathways.
https://www.bioconductor.org/packages/pathview
In pathview, you can do something like assuming your.data has Entrez Gene ID:

pv.out <- pathview(gene.data = your.data,
                pathway.id = "04320",
                species = "dme",
                gene.idtype = "ENTREZID")

In SBGNview, you can do a species specific pathway search like:

paths.dme <- findPathways(org = "dme")
head(paths.dme)

[greyman]

But when I use pathview, I cannot highlight Nodes/Metabolites of preference such as differentially expressed genes. It can only be achieved through SBGN view

[GenoMax]

greyman : Please create a new post with your questions about this tool.

This thread should be reserved as a original announcement of the package.

[greyman]

okay sure, can I still reply to this thread or I should start a new one now?

[neha.ghevaria3]

Hi, Can I use this package in offline mode without an active connect with some predownloaded files.

Answer 1

[bigmawen]

I installed the latest release version of SBGNview, and follow the tutorial
https://bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/SBGNview.Vignette.html
I tried compound data with either one column or two columns (samples). The output color slices are one and two correspondingly. So I was not able to replicate your problem. not sure what happened in your end.
BTW, I would suggest you install the latest version of SBGNview and SBGNview.data. you may need to update your Bioconductor and R too.

My code:

library(SBGNview)
data("sbgn.xmls")
data("pathways.info")
cpd.data <- sim.mol.data(mol.type = "cpd", 
                         id.type = "KEGG COMPOUND accession", 
                         nmol = 10000, 
                         nexp = 2)

SBGNview.obj1 <- SBGNview(cpd.data = cpd.data[,1],
                         input.sbgn = "P00001",
                         output.file = "test_output.cpd.1sample",
                         cpd.id.type = "KEGG",
                         output.formats =  "png")
SBGNview.obj1

SBGNview.obj2 <- SBGNview(cpd.data = cpd.data,
                         input.sbgn = "P00001",
                         output.file = "test_output.cpd.2sample",
                         cpd.id.type = "KEGG",
                         output.formats =  "png")
SBGNview.obj2

one sample output:

two sample output: