I used the Functional analysis based on Mummichog 2.0 + GSEA on the MetaboAnalyst 6.0 platform, but I think there is an error in the script to color the dots on the resulting pathway activity profile plot.
The legend mentions a red color for pathways whereby both GSEA and Mummichog are significantly altered, blue when it is only significant in Mummichog and green when it is only significant in GSEA. When I look at the output tables I have 3 pathways that are significantly altered in both Mummichog and GSEA. However in the exported plot, only one of these is colored red.
I tried to check if it might be a misinterpretation of the significant cut-off set for each P-value, but I couldn’t match the coloring with a meaningull cut-off in my data.
I would like to use this image for publication, and highly appreciate any help in figuring out why the plot and table doesn’t match.
Thank you!