Tutorial: Multi-omics data visualization with PathVisio

If you want to visualize different omics data types together on a pathway diagram, there are a couple of steps you need to follow. You first need to prepare your data file in the correct way (step 1), then you need to import your data (step 2) and lastly, you need to create an intuitive visualization (step 3).

Step 1: Prepare your data

All data needs to be combined in one data file. Very likely, you are using different identifiers for your different measurements (e.g. Entrez Gene for transcriptomics, UniProt for proteomics and ChEBI for metabolomics). Each identifier needs to be accompanied by the appropriate database/system code. Additionally, we advise to add a type column, indicating what data type/experiment the measurement comes from. The data file should look like this (with many more measurements per type).

Identifier System Code log2FC p-value Type
1636 L -1.2 0.02 Transcriptomics
P12821 S -0.8 0.04 Proteomics
CHEBI:3165 Ce -1.0 0.03 Metabolomics

You can also combine multiple transcriptomics datasets this way. If all identifiers are from the same database, the system code column is not needed.

Step 2: Import your data

After successful importing the data (identifiers were recognized), you should see some default visualization on the nodes with data.

Step 3: Create a visualization

Now it is important to create an intuitive visualization. As an example, we will create an advanced visualization and define a gradient-based visualization for the log2FC and a rule-based visualization for the Type.