Question: How to generate KEGG pathway classification chart
3
gravatar for dongchenchen
24 months ago by
dongchenchen30
dongchenchen30 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 • 4.2k views
ADD COMMENTlink modified 12 days ago by Leite1.1k • written 24 months ago by dongchenchen30

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 REPLYlink written 4 weeks ago by manhasjanvi110

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

ADD REPLYlink written 4 weeks ago by Shaminur150

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 REPLYlink written 4 weeks ago by dongchenchen30

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

Thanks

ADD REPLYlink written 4 weeks ago by Shaminur150

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

ADD REPLYlink written 12 days ago by deblinaroy164.19950
2
gravatar for Friederike
24 months ago by
Friederike6.8k
United States
Friederike6.8k wrote:

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

ADD COMMENTlink written 24 months ago by Friederike6.8k
1
gravatar for Clément Frainay
24 months ago by
Clément Frainay50 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 COMMENTlink written 24 months ago by Clément Frainay50
1
gravatar for jfo
24 months ago by
jfo40
jfo40 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 COMMENTlink written 24 months ago by jfo40

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

ADD REPLYlink written 9 months ago by fanimata0
0
gravatar for Leite
12 days ago by
Leite1.1k
São Paulo - Brazil - Unifesp
Leite1.1k wrote:

Dear

Maybe this can help:

Dotplot for filtered pathways result

Best, Leite

ADD COMMENTlink written 12 days ago by Leite1.1k
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