clusterProfiler - interpretation of enrichMap
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@jane-merlevede-5019
Last seen 3.0 years ago

Hello,

I am using enrichMap() on the results of enrichGO() and enrichDO() in clusterProfiler package. I would like some precisions and validations of what I understand from this map.

- a vertex represents a category ; its size represents the number of genes from the input that belong to this category - its colour represents the adjusted p-value showing the enrichment of this category. Is it possible to add a legend as in dotplot()?

- a edge represents the relationship between 2 categories. Does it represent the number of genes from the input shared between the 2 categories? Does the width of the edge represent the number of common genes between the 2 categories?

- Does it mean something when two edges intersect, with no common vertex between the edges?

- Do you have a hint to choose the number of vertices to plot or is it only based on how it looks?

Thank you in advance for your answers.

Jane

clusterprofiler • 1.7k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…
1. adding a legend in enrichMap is currently not supported. 2. Yes, if two categories have genes shared, there will be an edge connect them and the width of the edge is scaled by the number of common genes between them. 3. You can specify the number by enrichMap(n=X). But I don't have suggestion for the number of categories to be plotted.
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@jane-merlevede-5019
Last seen 3.0 years ago

Again, thank you for your answers.

- If I may come back to my third question, can you please tell me if it means something when two edges intersect?

I mean, when there are 2 independent networks (without a common vertex), they can be represented either separately or with an intersection. Does it mean something different?

 

- Can you please confirm that if two categories have genes shared among the genes from the input, there will be an edge connect them?

I mean, if 2 GO categories have common terms, but there is no gene from my input gene list common to the 2 GO categories, there won't be an edge between these 2 categories.

 

 

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maoqixing1 • 0
@maoqixing1-13732
Last seen 4.2 years ago

I want to know how to change the node size and highlight critical nodes in the enrichMap function?

Thank you!

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Currently, the only possibility is to save the enrichMap output to a igraph object and then by change the igraph object and re-plot again.

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