Reference for edge and node properties suitable for enrichMap{DOSE}
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@jansoderman-11752
Last seen 18 months ago

Hi,

I have used the enrichMap() function of the DOSE package to visualize enrichment results from the enrichPathway() function of the ReactomePA package. I assume that edge line thickness represent the overlap between connected nodes, that node color represent the significance of the enrichment and that node size corresponds to the number of differentially expressed genes in the gene set. However, I cannot find a description of this in the documentation of the DOSE or the ReactomePA package. Please provide a reference that describe the edge and node properties, and that is suitable for the enrichMap() function of the DOSE package.

Many thanks for any help and guidance.

DOSE ReactomePA enrichMap enrichPathway • 741 views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

Thanks.

All the visualization methods were re-implemented based on ggplot2, see https://github.com/Bioconductor/Contributions/issues/567.

In future release, legend of color, line wide etc will be provided.

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I do not understand how a reference to ggplot2 will help me understand the basis for the edge width, node size and node color. Could you please clarify your answer, while waiting for a release with an explanatory legend?
Sincerely/ Jan

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