How to explain the pathway distance？

[Rui-Jing]

Hi， CellChat does pioneering work comparing multiple databases about cell-cell communication. But I still have confused about the results of comparing multiple data sets. Just like the picture below: Larger distance implies larger difference of the communication networks between Database1 and Database2. So for this graph, can you explain whether database 1 is more enriched or database 2 is more enriched on some signaling pathways(eg WNT). In other words, Could it be said that dataset 1 enriched more on the WNT pathway and dataset 2 enriched less.

Another problem is that when I compare multiple datasets(>2), rankSimilarity and rankNet cannot show the differences from multiple datasets.

Looking forward to your kind reply.

[sqjin]

Hi @Rui-Jing , the pathway distance is computed based on the 2D-space. Thus it can indicate whether the same signaling between two datasets are similar or not. It cannot suggest whether it is enriched in one dataset. Based on the definition in rankSimilarity and ranNet, they definitely can only work for two datasets. But we provide a parameter in these two functions to allow for comparing any two pairs.

[Rui-Jing]

@sqjin Thanks for your answer. If I compare multiple datasets（>2）, what better way to show the differences between them? Because if multiple datasets are compared, the presentation mode of netVisual_embeddingPairwise and netVisual_embeddingPairwiseZoomIn are not clear enough to visually distinguish the differences.

[sqjin]

@Rui-Jing I would suggest to do it for any pair of two datasets. I am sorry I do not have a better solution for now.

[Rui-Jing]

@sqjin Hi, for a comparison of ligand-receptor pairs in two datasets, does it means a descending order of all different ligand-receptor pairs, or does it means a comparison of one of the ligand-receptor pairs in two datasets? Can you give me a demonstration ?(an example of comparison for L-R pairs).

[sqjin]

@Rui-Jing Sorry, I cannot well understand you.

[Rui-Jing]

@sqjin I'm sorry I didn't explain my question clearly. I was wondering if I could find the differences in specific L-R pairs when comparing cell communication between two databases. Or an overview of the difference in L-R pairs expression.

[sqjin]

@Rui-Jing If you follow the tutorial, you will find the generated cell-cell communication network for both signaling pathway and its associated L-R pairs. Then you can check the difference between specific L-R pairs. For the overall differences, please check our tutorial on comparison analysis. For the L-R expression, you can simply do it in Seurat.