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.