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Question: How to generate KEGG pathway classification chart
1
gravatar for dongchenchen
5 months ago by
dongchenchen • 10
dongchenchen • 10 wrote:

I have assigned KO numbers to my assembled transcriptome and would like to generate a KEGG pathway classification with x axis show gene numbers and percentage for each different terms. There seems exist a standard format for the chart that people use for publication. I would like to know the tool they use to makelike the one in the link this chart.
Thank you
rna-seq kegg • 592 views
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modified 5 months ago by Friederike ♦ 4.9k • written 5 months ago by dongchenchen • 10
2
gravatar for Friederike
5 months ago by
Friederike ♦ 4.9k
United States
Friederike ♦ 4.9k wrote:

I like clusterProfiler for this task, it provides fairly straightforward integration of both KEGG Pathway Enrichment Analysis as well as visualizations
ADD COMMENT • link written 5 months ago by Friederike ♦ 4.9k
1
gravatar for Clément Frainay
5 months ago by
Clément Frainay • 10
Clément Frainay • 10 wrote:

I don't know any tool that directly provides such chart, but that looks like base R plot to me.

Maybe people use KEGG mapper tool, like this one : https://www.genome.jp/kegg/tool/map_pathway.html

then format the results to be imported in R and use the barplot function https://www.statmethods.net/graphs/bar.html
ADD COMMENT • link written 5 months ago by Clément Frainay • 10
1
gravatar for jfo
5 months ago by
jfo • 10
jfo • 10 wrote:

This graph could definitely be generated using grouped bar plot in R (ggplot2).

To get the KEGG Pathways and their corresponding values, you should run KEGG reconstruction (https://www.genome.jp/kegg/tool/map_pathway.html) using your KOs. Format the resulting file to a table that will be used in R to generate the desired graph.
ADD COMMENT • link written 5 months ago by jfo • 10
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