Glad you succeed to solve your issue with Bash. To answer your question, you can define match_pat to be a vector of the column containing id files like `match_pat <- as.vector(list_id_file$NameOfTheColumWithID). Then, you can extract column form your GTEX brain sample file.

There is multiple examples of how to do heatmap with ggplot2 on SO, for example, you can start by taking a look here: stackoverflow.com/questions/8406394/… or stackoverflow.com/questions/14290364/… or stackoverflow.com/questions/60162198/… ... Try to reproduce those examples and then you will know how to deal with your data

That's a really weird (and interesting) result. Do you know if each package came with its own library of genesets ? Or are they all using the same ?

you should add a reproducible example of both dataframe (Cytokine and IL-17 signaling) by providing the output of dput(head(d)). It will make things easier for people trying to help you.