Pathway based data integration and visualization
  • Help
    • Overview
    • User Options
    • Custom Analysis
    • Example Analysis
    • API Documentation
    • References
    • Question?
  • Pathview
    • Bioconductor
    • Tutorial
    • R-Forge
    • Paper
  • About
  • Related
  • Login as Guest Account
    • Login
    • Register
    • Guest
  • User Home(current)
  • New Analysis
  • Example 1
  • Example 2
  • Example 3
  • Example 4
  • Help
  • API Help
  • API Query Generator
  • Questions?

Pathview API Documentation

Get Started

Pathview API (url) is a bash script. It depends on cURL which is already pre-installed with most Unix/Linux/Mac systems. cURL can be download here if needed. To get started:

1. Download API with cURL

curl -O https://pathview.uncc.edu/scripts/pathviewapi.sh

2. Modify access of the API

chmod +x ./pathviewapi.sh

3. Ready to go, please check the following sections for usage

Synopsis

Basic Usage

./pathviewapi.sh options --gene_data | --cpd_data [--gene_id] [-- cpd_id] [--pathway_id] ... [--other options]

Common Usages (Remove annotation in parentheses in real use)

   Gene data:

./pathviewapi.sh --gene_data your/gene/data/file --species hsa (KEGG species code) --gene_id ENTREZ (gene ID type) --pathway_id 00640 (KEGG pathway ID)

   Compound data:

./pathviewapi.sh --cpd_data your/ cpd/data/file -- cpd_id KEGG (compound ID type) --pathway_id 00640 (KEGG pathway ID)

   Gene and Compound data:

./pathviewapi.sh --gene_data your/gene/data/file --gene_id ENTREZ (gene ID type) --cpd_data your/ cpd/data/file -- cpd_id KEGG (compound ID type) --pathway_id 00640 (KEGG pathway ID)

   Pathway analysis with Gene and Compound data (can be one of them):

./pathviewapi.sh --gene_data your/gene/data/file --gene_id ENTREZ (gene ID type) --cpd_data your/ cpd/data/file -- cpd_id KEGG (compound ID type) --auto_sel T


Help

./pathviewapi.sh --help

Extras

   Detailed description of the arguments, click here

   Specific example analysis, click here

   Intuitive API query generator based on the GUI Web form, click here

   For extra issues, please contact pathomics@gmail.com


Example Analysis

Multiple Sample KEGG View

This example shows the multiple sample/state integration with Pathview KEGG view.

View details »

Multiple Sample Graphviz View

This example shows the multiple sample/state integration with Pathview Graphviz view.

View details »

ID Mapping

This example shows the ID mapping capability of Pathview.

View details »

Integrated Pathway Analysis

This example covers an integration pathway analysis workflow based on Pathview.

View details »

Options for the API (see GUI option page for details)

Flag Description Default(Common) GUI Options
Input/Output
--gene_data Gene Data accepts data matrices in tab- or comma-delimited format (txt or csv). (/home/data/gse16873.d3.txt) Gene Data
--cpd_data Compound Data accepts data matrices in tab- or comma-delimited format (txt or csv). (/home/data/sim.cpd.data2.txt) Compound Data
--gene_reference The column numbers for controls. Not needed if data is relative abundance (log ratios or fold changes). NULL(1,3,5) Control/reference
--gene_sample The column numbers for cases. Not needed if data is relative abundance (log ratios or fold changes). NULL(2,4,6) Case/sample
--gene_compare Whether the experiment samples are paired or not. Not needed if data is relative abundance (log ratios or fold changes). paired Compare
--cpd_reference The column numbers for controls. Not needed if data is relative abundance (log ratios or fold changes). NULL(1,3,5) Control/reference
--cpd_sample The column numbers for cases. Not needed if data is relative abundance (log ratios or fold changes). NULL(2,4,6) Case/sample
--cpd_compare Whether the experiment samples are paired or not. Not needed if data is relative abundance (log ratios or fold changes). paired Compare
--suffix The suffix to be added after the pathway name as part of the output graph file name. pathview Output Suffix
--auto_sel Whether to select pathways manually or through pathway analysis. If set to T (or TRUE), --pathway_id option will be ignored. F Pathway Selection
--pathway_id The KEGG pathway IDs, usually 5 digit long.Pathway IDs can also be provided in a comma separated file.This option is not needed when --auto_sel is T (or TRUE). 00010(00010,00640) Pathway ID
--gene_id ID type used for the Gene Data. ENTREZ Gene ID Type
--cpd_id ID type used for the Compound Data. KEGG Compound ID Type
--species Either the KEGG code, scientific name or the common name of the target species. Click GUI dropdown for Species if not sure. hsa Species
Graphics
--kegg Whether to render the pathway as native KEGG graph (.png) or using Graphviz layout engine (.pdf). T Kegg Native
--layer Controls plotting layers. Check the GUI option page for details. F Same Layer
--split Whether split node groups are split to individual nodes. F Split Group
--expand Whether the multiple-gene nodes are expanded into single-gene nodes. F Expand Node
--multistate Whether multiple states (samples or columns) Gene Data or Compound Data should be integrated and plotted in the same graph. T Multi State
--matched Whether the samples of Gene Data and Compound Data are paired. T Match Data
--discrete_gene Whether Gene Data should be treated as discrete. F Discrete Gene
--discrete_cpd Whether Compound Data should be treated as discrete. F Discrete Compound
--keyposition Controls the position of color key(s). topleft Key Position
--signatureposition Controls the position of pathview signature. bottomright Signature Position
--offset How much compound labels should be put above the default position or node center. 1.0 Compound Label Offset
--align How the color keys are aligned when both Gene Data and Compound Data are present. Potential values are x and y. x Keys Alignment
Coloration
--limit_gene The limit values for Gene Data when converting them to pseudo colors. 1(-1,1) Limit Gene
--limit_cpd The limit values for Compound Data when converting them to pseudo colors. 1(-1,1) Limit Compound
--bins_gene The number of levels or bins for Gene Data when converting them to pseudo colors. 10 Bins Gene
--bins_cpd The number of levels or bins for Compound Data when converting them to pseudo colors. 10 Bins Compound
--node_sum The method name to calculate node summary given that multiple genes or compounds are mapped to it. Potential values can be found in Node Sum drop down list in GUI. sum(mean) Node Sum
--na_color The color used for NA's or missing values in Gene Data and Compound Data. Potential value can be transparent or grey. transparent NA Color
--low_gene /--mid_gene / --high_gene The color spectrum to code Gene Data.Hex color codes can also be given (#00FF00, #D3D3D3). green/gray/red Low,Mid,High Gene
--low_cpd / --mid_cpd / --high_cpd The color spectrum to code Compound Data.Hex color codes can also be given (#00FF00, #D3D3D3). blue/gray/yellow Low,Mid,High Compound
API Specific
--username The registered email to access the API. guest NA
--password The password for the registered account to access the API. NULL NA

Output from API

If API query succeeds, it will generate a url in json format for results download.

Example: {"download link":"http://pathview.uncc.edu//all/demo/57b61a93e1fab/file.zip"}

If any problem occurs, the API will throw error messages or warnings, which are usually self-explanatory.

Implementation

Pathview Web API is RESTful as it adheres to the REST (Representational State Transfer) architecture. In particular, this API (1) is stateless, (2) use base URLs to its resources (3) supports standard HTTP methods (e.g. GET, POST, etc) , and (4) returns its responses in JSON format. Pathview Web API currently supports HTTP queries through POST but not GET. While GET method is often used directly in a web browser for data retrieval (in URL format), POST method allows more complex queries with user input data and options (through command-line like statements). Pathview Web API and GUI have different front ends (command line vs web page) and response formats (JSON vs HTML), but they share the same backend. The key difference between here is that they use different Controllers in the Laravel MVC (Model-View-Controller) framework (details at https://laravel.com).

Reference

Please cite our paper if you use this website. This will help the Pathview project in return.

  • Luo W, Pant G, Bhavnasi YK, Blanchard SG, Brouwer C. Pathview Web: user friendly pathway visualization and data integration. Nucleic Acids Res, 2017, Web Server issue, doi: 10.1093/ nar/gkx372
  • Luo W, Brouwer C. Pathview: an R/Biocondutor package for pathway-based data integration and visualization. Bioinformatics, 2013, 29(14):1830-1831, doi: 10.1093/bioinformatics/btt285

Please also cite GAGE paper if you are doing pathway analysis besides visualization, i.e. Pathway Selection set to Auto on the New Analysis page.

  • Luo W, Friedman M, etc. GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 2009, 10, pp. 161, doi: 10.1186/1471-2105-10-161

Contact

Email us: pathomics@gmail.com

© 2013 -       Pathview Project

Bioinformatics Services Division - Department of Bioinformatics and Genomics - UNC Charlotte