Hi, I have expression of genes in two different groups of patients, I want to do pathway analysis and know which processes are effected by my genes, I know about enrichr, kegg, reactome and so on. I don't know if I am allowed to share this figure, but I want a figure like this! I searched a lot for it but couldn't find how to draw this chart. Thanks
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dark_rider_2010 •
The figure you linked to is just a set of horizontal bar charts. Just plot your counts in each pathway as a bar plot in R using the barplot() function with the horiz = TRUE option. Colour as you need with e.g. col = c("red", "blue").
I just don't know how to connect output of kegg (or any other databases) to this.
Simply count the number of genes of interest that fall into each pathway. This is usually available from the software with which you've done the enrichment analysis, e.g. the web-based enrichr exported table has this in the overlap column or in the genes column as a list of input genes that fall into the corresponding GO term or pathway.
This post might be also useful to you,
Gene ontology comparsion between up- and down-regulated genes
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