I would like to ask if anybody has an idea about visualizing the gene ontology on R using bubble plot as shown in Fig 3 of this report? https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evu070 I am analyzing a data of transcriptomic analysis of a dimorphic fungus by comparing the expression pattern during the yeast growth and hyphal growth. This bubble plotting will be perfect in showing my data as I can insert the data of both growth forms into one plot for easy comparison instead of visualizing them separately. The authors of this work said that they performed it using Python script makeDendrogram.py) in (pyEnrichment). As I am not familiar with Python, I could not be able to use it. I will be grateful to anybody can help me to apply such bubble plot on R. Any similar plot can accomplish my goal is also OK. Thanks for the help in advance.
Check out GeneSCF
Representation figures in GeneSCF article: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1250-z
Hi, you can plot similar representations in clusterProfiler; "https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html".