Question: Visualization of Gene Ontology using bubble plot.
0
gravatar for Agamy89
19 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 • 2.9k views
ADD COMMENTlink modified 21 days ago by patrick.kraetschmer10 • written 19 months ago by Agamy890
2
gravatar for EVR
19 months ago by
EVR540
Earth
EVR540 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 19 months ago by EVR540
1
gravatar for EagleEye
19 months ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Check out GeneSCF

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

ADD COMMENTlink written 19 months ago by EagleEye6.4k
0
gravatar for Puli Chandramouli Reddy
19 months ago by
Pune, India
Puli Chandramouli Reddy180 wrote:

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

ADD COMMENTlink written 19 months ago by Puli Chandramouli Reddy180

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 19 months ago by Agamy890

Can you post your topGO output.

ADD REPLYlink written 19 months ago by Puli Chandramouli Reddy180

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

Thank you in advance, Andrew

ADD REPLYlink written 11 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 10 months ago by Puli Chandramouli Reddy180
0
gravatar for patrick.kraetschmer
21 days ago by
patrick.kraetschmer10 wrote:

Why not try this R-based package: bubble plots and more elaborate GO visualisations are contained within it and relatively easy executed: https://wencke.github.io/

ADD COMMENTlink written 21 days ago by patrick.kraetschmer10
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