Visualise Metabolic Networks

Select reactions to visualise

Fill the Cart with reactions

The visualisation is performed on the reactions present in the Cart grid localised in the right-side panel. Select a set of reactions in the reaction grid. There are two ways to fill the cart:

  • Right-click on the grid and select "Copy Selection to Cart" to copy them in the Cart grid."Copy All to Cart" if you want to copy all the reactions in the Cart.
  • Drag and drop the selection in the Cart grid. For this, open the Cart panel, hold down the selection and drag it to the Cart table.

Copy reactions with the right-click menu or by drag&drop from Reaction grid to the Cart.

Handle the Cart data

Remove data from the Cart

Empty cart

To remove all the reactions from the Cart, right-click on the grid and select "Empty Cart".

Delete selected reactions

Select some reactions in the Cart grid (hold Ctrl for selecting several rows), right-click on the grid and select "Delete Selection".

Delete no flux reactions

By clicking on the button "Delete Flux=0", reactions for which the flux lower and upper bounds equal to 0 are removed from the Cart. Note that no flux analysis is done here, only flux bounds indicated for each reaction are taken into account.

Filter from the Cart grid

Propagating filter can be performed from the Cart grid, as for other data grids.

Online visualisation with MetExploreViz

Launch the visualisation with MetExploreViz

There are two ways for drawing the network corresponding to the reactions in the Cart:
  • Right-click on the Cart grid and select "Create network in viz from Cart". Then go to the "Network viz" panel.
  • Go to the "Network Viz" panel and select "Load Network from website"

Visualise and tune the design of the network with MetExploreViz

Consult the documentation of MetExploreViz to learn how to manage the drawing of the network and explore it.

Visualise omics data mappings

if an omics data mapping has been performed in MetExplore, mapping selection appears in the "Network Manager" window of MetExploreViz in the Omics panel. Please consult documentation of MetExploreViz to learn how to visualise mapping data on the network.

Links between MetExplore grids and MetExploreViz nodes

Select rows in grid from network nodes

Right-click on a node in MetExploreViz and click on "Select nodes" and then on "Only this node" for selecting the corresponding row in the Metabolite or Reaction grid. Click on "All the nodes" if you want to select all the rows corresponding to selected nodes in the Metabolite or/and Reaction grids.

See node information

Right-click on a node in MetExploreViz and click on "See more information". A window information will be displayed containing MetExplore data associated to this node.

Network in MetExplore. The contextual menu on a node and an information window are displayed.

Highlight nodes from grids

To highlight nodes from Reaction or Metabolite grid:
  • Select corresponding rows in the grid
  • Right-click on the grid
  • Select "Highlight in visualisation"