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YuLab-SMU / enrichplot

Visualization of Functional Enrichment Result
https://yulab-smu.top/biomedical-knowledge-mining-book/
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show all nodes but show select labels in emapplot #257

Open SMM02 opened 1 year ago

SMM02 commented 1 year ago

Hello,

How can I modify the emapplot command to show all nodes(categories) but label only some of them? Specifying categories in "showCategory" labels those but removes all other nodes as well.

For example, if there are enriched terms, "protein targeting", "protein targeting to membrane" and "protein targeting to ER", I want to show all 3 modes connected to each other but with only "protein targeting" labeled.

Thanks!

Best, Salwa.

huerqiang commented 1 year ago

There are currently no parameters to achieve this purpose, and we may support it later.

SMM02 commented 1 year ago

Hello, thank you for your reply! Instead of labeling selected terms, is there a way to remove all labels and only keep the nodes?

Also, I ran an enrichGO for GOBP and 125 terms were enriched. When I ran pairwise_termsim and then emapplot(GOBP), only about 30 terms were randomly plotted. Why were these 30 terms shown and not all of them? Some of my terms had 2 counts and some had 14, but the "number of genes" were 3 to 12.

Thanks!

SMM02 commented 11 months ago

Hello, I realized I could include argument node_label="none" to remove all labels while keeping the nodes. If this argument could be modified so specific categories can be labelled instead of "all" or "none", that would be really helpful. Thanks!