User documentation

General functioning

MetExploreViz is a tool to visualize metabolic network. It allows to map "omics" data and to interact with metabolic networks. It is usable as a javascript library via the MetExplore web server or within your website.

MetExploreViz works by taking as input:

JSON must have a particular format to work in MetExploreViz. The format of this JSON must follow this template:
    {
        nodes:
        [
            {
                "name":"RE1473",
                "dbIdentifier":"R_RE1473C",
                "ec":"2.3.2.2",
                "id":"938355",
                "reactionReversibility":true,
                "biologicalType":"reaction"
            },
            {
                "name":"Coenzyme A",
                "compartment":"m",
                "dbIdentifier":"M_coa_m",
                "id":"1109601",
                "isSideCompound":false,
                "biologicalType":"metabolite",
            }
        ],
        links:
        [
            {
                "id":"938355 -- 1109601",
                "source":1,
                "target":0,
                "interaction":"in",
                "reversible":"true"
            }
        ]
    }
    


Soon other attributes can be used to have more informations on the visualisation.

Visualisation from JSON file

To used a JSON file you should use the browse button on the top left corner. Choose a JSON file which follows MetExploreViz requirement. And the visualisation will be launched.

Basic features

After created the network representation, you will be able to:

  • Move or zoom in the drawing via mouse interactions;
  • Once the algorithm is providing a relevant drawing you can pause the animation.

Mouse interaction: Zoom and pan

Panning: By pressing the mouse wheel you can then translate the drawing.
Zooming: using mouse wheel you can zoom in and out. Zoom will be centered on the mouse position

We also provide zoom for laptop mouse pads.
  • Zoom in the drawing via this button:
  • Zoom out the drawing via this button:
  • Pan the drawing via this button:

Force directed animation

The default way to draw the metabolic network is by using a force directed algorithm. This algorithm simulates a forces on edges between nodes. It allows animation.

Click on the button to stop the animation.

Click on the button to start the animation.

Interactive visualisation

MetExploreViz provides direct interactions with nodes. So, you can:

  • Remove node with right click;
  • Select node by:
    • clicking on node;
    • grouped selection.
  • Select a node and its nearest neighbours by clicking on node with "N" key:
  • Drag and drop nodes. You can also move all selected node with "ctrl" key.

Remove node

MetExploreViz provides a function to remove nodes with right click.

Mining networks

Networks may be quite dense and can involve reactions and metabolites that are of no interest for the current study. To lower the complexity of the representation we are developing “mining” methods based on graph algorithms.

The aim is, given a set of nodes, to try to compute relevant paths between each pair of nodes. A path is a set of reactions that allows to go from one element in the network to another.

Remark: not that reactions can be used only once, avoiding artificial loops on paths.

This function can have two kinds of inputs:

  • A selection of nodes: by left clicking on nodes you can select some of them and then start the computation;
  • Mapped data: if there is no manual selection, nodes with mapped data will be used for the computation.

Highlight subnetwork

When you launch this, subnetwork is hithlighted, links and nodes absent from the subnetwork become transparent.

Extract subnetwork

This function allows to keep only links and nodes in the subnetwork. All other will be removed.

Drawing

To ease visualization and interpretation of metabolic networks, MetExploreViz allows to duplicate or remove side compounds, change nodes position or highlight compartments or pathways.

Side compounds

In metabolic networks compounds are considered of variable important in metabolism flow. Taking into account this heterogeneity is important to avoid interpretation mistakes and to facilitate visualization. MetExploreViz allows to:

  • Duplicate side compounds;
  • Remove side compounds.

To do this the attribute value "isSideCompound" of metabolite must be set to "true", and the action can be picked from the drawing menu.

Layouts

To group substrates and products on each side of a reaction, click on "Reaction components direction" in the drawing menu.

When compartments or pathways are highlighted it's possible to clust nodes by these components.

Export

These functions allow you to export the visualization in SVG, PNG or JPG.

Import

You can import files to enrich your network.

Mapping

The mapping import allows you to import data on metabolites or reactions and highlights/colors the nodes according to the provided numerical values.

First you could import tab file with some requirements:

  • "identifier"
  • "conditionName."
  • "identifierN."
  • "x" values

identifier    conditionName1  conditionName2 ...
    identifierN1   x    x1 ...
    identifierN2   x2   x3 ...
    identifierN3   x4   x5 ...
    identifierN4   x6   x7 ...
    


"identifier" allows MetExploreViz to identify the corresponding nodes. The following identifiers are currently supported:

  • "reactionDBIdentifier"
  • "metaboliteDBIdentifier"
  • "inchi"
  • under development:
    • "name"
    • "your attribute"

"conditionName." can arbitrarily chosen.

"identifierN." allows to MetExploreViz to recongnize nodes on data.

"x" are the values given to one component under each condition.


In order to import your file, click on mapping button.

After choosing a file, MetExploreViz maps values on nodes and open the "Network Manager" window.

Select a mapping imported and the nodes mapped are highlighted.

Then select a condition, values type and click on the button.

Depending on the data type, colors are assigned to nodes according to numerical values.


For discrete values, a color is assigned to each value.

For continuous values, a gradient from yellow to blue is created and each node color is assigned accordingly.

Minimum
Maximum

Flux

For flux values, a gradient from yellow to blue is created and each node color is assigned accordingly and values are assigned to links.

Minimum
Maximum

It is possible to change colors. To do this change the hexadecimal value or select a color in the color picker, and click on refresh button .

Side Compounds

The side compounds import allows you to assign metabolites as a side compounds. After this import, it's possible to duplicate side compounds. The text file must contain metabolite identifiers.



Save

These functions allow you to save the visualization in JSON, DOT or GML.

  • JSON can be used to save your work. It can be reloaded in MetExploreViz.
  • DOT and GML are simple ways of describing graphs that both humans and computer programs can use.

Customization

MetExploreViz allow you to custom your visualization.

  • MetaboliteStyle - To manage the height, width, rx, ry, font size, stroke width, display node name, stroke color of metabolites
  • Reaction style - To manage the height, width, rx, ry, display node name, font size, stroke color, stroke width of reactions

Optimization

For big network network drawing can be long. To optimize this you can remove some components during drawing. You can fix a threshold on the number of nodes and when this threshold is exceeded selected components are removed.

Network comparison

MetExploreViz allows the comparison of a metabolic network under several conditions.

Duplicate network

It is possible to duplicate network in another frame to visualise separately two conditions.


To do this click on this button and give a name to the network.

Link and compare representations

After duplication you can link by clicking this button the two representations of network to have the nodes in the same position of the original graph. If data have been mapped onto the original network the same colors are assigned to the nodes. So you can compare easily a network with different data.

Example

Search node

MetExploreViz allows you to search nodes in metabolic network.

To do this, enter the name, id, compartment of a node and click on the "search" button .

Set node name

MetExploreViz allows you set node name in visualisation.

To do this right click on a node and select 'Change name' menu.

Set select neighbours

MetExploreViz allows you select neighbours of a node in visualisation.

To do this right click on a node and select 'Select neighbours' menu.