Hi

I have done differential expression in a treatment versus control and fed my differentially expressed genes to plot a KEGG pathway by pathview where I obtained this

![enter image description here][1]

I have selected `for visualization because that was very significant. For example I knowCXCL1is being highly up regulated in my treated group;CXCL1` has been coloured by red here; What does that mean please? Actually I was not able to understand the colour scheme in this plot. Can you please help me?

Thanks a lot in advance

I

The red colour relates to precisely what you have said, i.e., the fact that CXCL1 has heightened expression levels in your data and is up-regulated in your treated group. Conversely, green, in this case, would indicate low expression / down-regulation.

However, the precise interpretation of the colour scale depends on the input data that you provide to pathview: If you provide a data-matrix of expression values, then the colour scale relates to high|low expression. If you supply fold-changes, then it relates to fold-change differences. You can technically supply any values that you want to pathview.

You can modify the limits of the scale to suit the input data that you provide. Please read the manual and vignette to see how to do this.

Kevin