Check our iPath user interface tutorial.
Main parts of iPath's user interface are shown in the image on the right.
Identifiers and names of following data types will be searched:
Check our map customization video tutorial.
iPath provides powerful data mapping tools and extensive customization options. Customize tab in the in the controls panel (shown on the right) provides access to all available customization options. Hover your mouse cursor over individual options to see a short explanation. Various options are described in detail below:
Three parameter types are supported:
C00001 #0000ff W20 0.5 K00824 #00ff00 R09112 #ff0000 W10
In the example above, all map elements which contain water (KEGG compound ID C00001) will be colored blue (#0000ff), half transparent (opacity 0.5) and have width/radius 20px (W20). Elements which are associated with KEGG orthoulogous group K00824 will be colored green (#00ff00), fully opaque and use the default width. Elements which are associated with KEGG reaction R09112 will be colored red (#ff0000), fully opaque and have width/radius 10px (W10).
The following data types are supported by iPath, and can be used to customize the maps. Make sure you use the required prefix for each data type, as shown in the examples below.
|Data type||Prefix||Example ID|
|Enzyme EC numbers||E or EC||E18.104.22.168|
|NCBI GI IDs||NCBI-GI:||NCBI-GI:326314893|
Click on any number in the table to highlight the corresponding edges/nodes.
When multiple IDs with different parameters in your selection match the same element in the map, a conflict occurs. Clicking on any edge/node where a conflict is present will display a table similar to one shown on the right. A list of conflicting IDs and their customization parameters is shown, with the keyword 'current' highlighting the currently applied parameters. Clicking the 'Select' button next to any ID will apply its customization parameters to the selected element. You can also apply the customization to all matching edges/nodes by clicking the 'All' button.
If a Selection title is specified when submitting data, all selection parameters will be stored, and can be simply accessed through the "Saved selections" box. Saved selections are tied to the current iPath overview map. If you switch to a different map, customization data must be submitted again. Currently active selection will be highlighted with a green box. Use the function icons next to each saved selection name to:
Use the time series functions to simply create an animation based on your map customizations. To create a time series animation:
Currently playing animation can be paused by clicking the play/pause button, or stopped completely by clicking the stop button.
Customized maps in iPath can be saved in various output formats. Clicking the 'Export' tab in the control panel to access the export function. Maps can be exported into any of the following formats:
Note: Due to technical limitations, transparency cannot be preserved in EPS and PDF formats.
Check our iPath account video tutorial.
Creating an account in iPath gives you the possibility to easily organize your element selections and access them from any browser. Selections are grouped into different projects, and these can be arranged into different workspaces.
Configuration and functions can be accessed by clicking the icons in the corner of project boxes, in the workspace tab bar and at the end of each selection table row.
Working with projects and workspaces:
An example dataset file is available for download, which maps the enzymatic activity in the human gut microbiome (metagenomic data derived from Japanese fecal samples). First, second and third columns represent 1:ortholog ID in KEGG, 2:abundance of the OG (represented using element width, 'W') and 3:color in the map respectively. Simply paste the contents of the file into iPath's element selection box, and set map background color to black for best results.