Making protein protein interaction figure

Question

[shahbaz.ahmed]

Hello All,

I have a protein-protein interaction dataset in the form of an excel file that was generated from an RNA-seq dataset using DEGs. It has 5 different columns 1: node1_protein, 2: node2_protein, 3: node1_gene, 4: node2_gene, and 5:score. I wanted to make a figure as we get in a string consisting of a central node and interacting proteins, Could you please help me in making that figure with such a dataset, I tried looking into string if it takes such a dataset but could not find anything. Please let me know if there is any online tool or R package that does it

Thank you so much for helping

Answer 1

[Pierre Lindenbaum]

Could you please help me in making that figure with such a dataset, I tried looking into string if it takes such a dataset but could not find anything.

use graphviz dot with a text file: https://graphviz.org/documentation/

to create a simple graph do something like (not tested):

awk 'BEGIN { printf("digraph G {");} {printf("%s -> %s ;\n",$3,$4);} END {printf("}\n");} input.tsv | dot -T png -o out.png