How to generate KEGG pathway classification chart

Question: How to generate KEGG pathway classification chart

24 months ago by

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 make like the one in the link this chart.
Thank you

rna-seq kegg • 4.2k views

ADD COMMENT • link •

modified 12 days ago by Leite • 1.1k • written 24 months ago by dongchenchen • 30

Hi @dongchenchen, was wondering if you were able to crack the R-code for this KEGG pathway classification chart. Pls post it here in case you were able to make one Thanks!

ADD REPLY • link written 4 weeks ago by manhasjanvi11 • 0

Hi, I think python package might help to draw such like of image.

ADD REPLY • link written 4 weeks ago by Shaminur • 150

Yes. I was able to generate the graph live above. For the plotting part, Excel is enough. ggplot for R or Matplotlib for Python would do fair job as well. My initial difficulty was to prepare data ready to generate graph from the raw annotation exported from KEGG website. I wrote a python script to group the annotation result in desired level (B level in my case). And then did the counting after uniquely sorted them.

ADD REPLY • link written 4 weeks ago by dongchenchen • 30

If you don't mind, share your details working script here!

Thanks

ADD REPLY • link written 4 weeks ago by Shaminur • 150

In case when multiple genome sequences used.. how to interprete the data from KEGG plot and COG plot?

ADD REPLY • link written 12 days ago by deblinaroy164.1995 • 0

24 months ago by

Friederike ♦ 6.8k

United States

Friederike ♦ 6.8k 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 24 months ago by Friederike ♦ 6.8k

24 months ago by

Clément Frainay • 50

Clément Frainay • 50 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 24 months ago by Clément Frainay • 50

24 months ago by

jfo • 40

jfo • 40 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 24 months ago by jfo • 40

Hi! How can I download the results from KEGG mapper and format it for plotting it in R.

ADD REPLY • link written 9 months ago by fanimata • 0

12 days ago by

Leite • 1.1k

São Paulo - Brazil - Unifesp

Leite • 1.1k wrote:

Dear

Maybe this can help:

Dotplot for filtered pathways result

Best, Leite

ADD COMMENT • link written 12 days ago by Leite • 1.1k

Please log in to add an answer.

Similar posts • Search »