How to generate KEGG pathway classification chart

Question

[dongchenchen]

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 this chart.
Thank you

[manhasjanvi11]

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!

[MSRS]

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

[dongchenchen]

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.

[MSRS]

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

Thanks

[microecologist93]

Has anyone been able to create the script for this annotation of the hierarchies?

[deblinaroy164.1995]

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

Answer 1

[Friederike]

I like clusterProfiler for this task, it provides fairly straightforward integration of both KEGG Pathway Enrichment Analysis as well as visualizations

Answer 2

[Clément Frainay]

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

Answer 3

[jfo]

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.

[fanimata]

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

Answer 4

[Leite]

Dear

Maybe this can help:

Dotplot for filtered pathways result

Best, Leite