Question: Visualization of Gene Ontology using bubble plot.
0
gravatar for Agamy89
13 months ago by
Agamy890
Agamy890 wrote:

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.

sequencing rna-seq R • 1.8k views
ADD COMMENTlink modified 13 months ago by Puli Chandramouli Reddy150 • written 13 months ago by Agamy890
2
gravatar for EVR
13 months ago by
EVR510
Earth
EVR510 wrote:

HI Agamy89,

I generally use REVIGO for visualizing the GOs. The best part of revigo is that all its plots are generated in R and you can download the R script and work on it to suit your needs

ADD COMMENTlink written 13 months ago by EVR510

Thanks a lot for your advice. It could work in my case.

ADD REPLYlink written 12 months ago by Agamy890
1
gravatar for EagleEye
13 months ago by
EagleEye6.0k
Sweden
EagleEye6.0k wrote:

Check out GeneSCF

Representation figures in GeneSCF article: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1250-z

ADD COMMENTlink written 13 months ago by EagleEye6.0k

Thank you for your advice.

ADD REPLYlink written 12 months ago by Agamy890
0
gravatar for Puli Chandramouli Reddy
13 months ago by
Pune, India
Puli Chandramouli Reddy150 wrote:

Hi, you can plot similar representations in clusterProfiler; "https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html".

ADD COMMENTlink written 13 months ago by Puli Chandramouli Reddy150

Thank you for your suggestion. Actually, the form of visualization using clusterProfiler package is perfect in one of my cases; I performed several soft clustering and wanted to compare their GO in one graph instead of several graphs. However, I find difficulty to visualize my GO using clusterProfiler as I am using topGO package for GO enrichment and it seems that the output of TopGO is not working with clusterProfiler. If you know the way to input topGO output in clusterProfiler package, I will be thankful to you if you provided to me. Thank you in advance.

ADD REPLYlink written 12 months ago by Agamy890

Can you post your topGO output.

ADD REPLYlink written 12 months ago by Puli Chandramouli Reddy150

Dear Puli, Did you get to solve this? If so, could you please share your solution?

Thank you in advance, Andrew

ADD REPLYlink written 4 months ago by georomano0

I have not received the input file Agamy89 has used to test. If you are facing the same problem, post the input.

ADD REPLYlink written 4 months ago by Puli Chandramouli Reddy150
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