This document provides instructions for visualizing metabolic networks using the MetaMapp R package and Cytoscape software. It describes how to: 1) Prepare input files for MetaMapp and address common errors, 2) Obtain network and node attribute files from MetaMapp, 3) Import these files into Cytoscape and visualize the network using various layouts, 4) Map node attributes such as color, size, and label to experimental metadata, and 5) Manipulate the network view through filtering, clustering, and exporting for publication. The goal is to create clear, focused visualizations of metabolic subnetworks from omics data.

1. Unit 5.2
Metabolic network
visualization (exercise)
Dinesh Barupal
dinkumar@ucdavis.edu

2. Input file :
MetaMapp R-
Package (openCPU
version)
Network file
Node attribute file
How to use MetaMapp ?

3. How to use MetaMapp ?
Prepare the input file.
Example :
TeachingMaterialDataSetsBioinformatics_Training_DataMetaMappNull_MetaMapp_input.xlsx

4. MetaMapp input file errors -
• Duplicate PubChem CIDs
• Duplicate names
• Missing SMILES codes
• Missing p-value or fold-change
• Headers mismatch
• > 1000 compounds

5. How to use MetaMapp ?
Obtaining the MetaMapp files.
• Go to http://metamapp.fiehnlab.ucdavis.edu
Copy and paste your data
in this box
Click here
Now, click on these two buttons
chemsim_krp_07.sif node_attributes_chemsim_krp_07.tsv
Both files are provided in the training data folder for the case study.

6. chemsim_krp_07.sif
node_attributes_chemsim_krp_07.tsv
Structure of the created files.
Both files will be imported in the Cytoscape
software for visualization
KRP – KEGG Reaction Pairs – biochemical relationships
TMSIM – Tanimoto similarity – chemical relationships

7. What is Cytoscape ?
The most used network visualization and analysis tool.
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1001843http://www.cytoscape.org/
Backed by strong institutions

8. Visualize a range of experimental data on a
network graph
Useful graph layout algorithms
Graph theory calculations
Easy organization of multiple networks for
comparisons.
Faster navigation of large networks
Filter and query the network
Contributed plugins
Works on PC, Max and Linux system
USB drive contains a copy of Cytoscape software
Cytoscape basic features

9. Start Cytoscape software
Locate the chemsim_krp_07.sif file and click import.
The file shall be in your download folder or you can use
the file in the example folder.
How to use Cytoscape?

10. Visualization panel
Table panel highlights the data related to selected node
(yellow).
Cytoscape windows

11. Useful buttons in the menu-bar
Zoom in Zoom out Zoom-all
Zoom in
selected
You will use these often.

12. Show graphics details
Tip: if you don’t see the labels/edges/shapes/colors in graph, click on “Show graphics details”.

13. Visualize using the yFiles (organic layout). You can try other layout methods, but this one is recommended.
Layout a network graph

14. Now import your Node Attributes file

15. Import your Node Attributes file

16. Import your Node Attributes file
“Key” symbol
should be
PubChem_ID

17. Import your Node Attributes file
Table panel after importing the node attributes.

18. Data visualization
All visual properties
can be accessed in the
style tab.
Node color
Node size
Node label
Node label position
Node Label font size
Edge color
Edge width
Network background color
Left bottom corner

19. Change network background color
1
2
3
Select black background color or any color you like.

20. Switch back to the node visual properties
Click on the node tab.

21. Double click here
click here
Node coloring : “Node Fill color”

22. Red = higher in
male mouse
Blue = higher in
female mouse
Yellow = no
change
Node coloring : “Node Fill color”

23. Change node label
You can choose any
label from the node
attribute file.
You need to zoom in to see the labels
Use the scroll button to zoom in
and out.

24. If you don’t see the labels

25. Intermediate network graph
 crowded, overlapping labels and unpublishable.

26. Change label font size
Showing labels for only the significant compounds.
It is bit clearer.

27. Change node size
Select the values by press the left click
on mouse. Then right click.
Node size rules
FC 1.0 – size = 20
FC >1 & <2 --size = 60
FC >2 & < 3 -- size = 100
FC >3 & < 5 --size = 150
FC > 5-- size = 200

28. Visualize using the yFiles (organic layout). You can try other layout methods, but this one is recommended.
Apply the organic layout
 Not yet
publication ready

29. Node moving
Press “control” key and click left
mouse button and select the area
Now you can move
these nodes

30. Change edge colors
This box must be checked.
The visual property is
under the subtab – “edge”

31. Intermediate network graph
Lipids
Amino acids
and amines
sugars
nucle
 Not yet
publication ready

32. Cluster detection
Check this box
Large network can be divided into smaller modules for better
visualization and interpretation

33. Clustered network

34. Clustered network
Phospholipids
TG, DG, MG, FA
CEs
Nucleotides
Aromatics
Peptides
Sphingolipids Amino acids

35. Create a sub-network
Select a cluster by pressing “Ctrl” and
then left click and make a square
box.
Once selected the nodes,
Prese Ctrl+N to make a new network
Show graphics
details

36. Node label position
Click on the label position
It will make label position property
available in the style tab.

37. Select right side nodes
Click on this box to
change the property
for selected node.
Drag the
object box
to the left
and click ok
Node label position

38. Select left side nodes
Click on this box to
change the property
for selected node.
Drag the
object box
to the left
and click ok
Node label position

39. Increase the scaling factor to
remove the overlaps of labels.
Scaling
Focused view of the phospholipid cluster.

40. Network navigation
Click on a network you want to visualize
Create
subnetworks for –
• Sphingolipids
• Cholesteroyl esters
• TGs
• Phopspholipids
• One carbon metabolism

41. Phospholipids cluster
Cholestroyl esters
Sphingolipids and amino acids
Focused visualization of clusters
Clearer, readable, less crowded.
This can go in a paper. 

42. Save the session for future

43. Export the network as a pdf file