Question: Reference for edge and node properties suitable for enrichMap{DOSE}
0
gravatar for jan.soderman
20 months ago by
jan.soderman0 wrote:

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.

ADD COMMENTlink modified 20 months ago by Guangchuang Yu1.1k • written 20 months ago by jan.soderman0
Answer: Reference for edge and node properties suitable for enrichMap{DOSE}
0
gravatar for Guangchuang Yu
20 months ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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.

‚Äč
ADD COMMENTlink written 20 months ago by Guangchuang Yu1.1k

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

ADD REPLYlink written 20 months ago by jan.soderman0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 155 users visited in the last hour