Geneset visualisation pipeline

Quinten Plevier, Stage TNO

Last update: 04-06-2024

User input

Make a folder data/user_input/ where you put your count data with filetype .tsv and your metadata with filetype .txt. Change the folders in config/config.yaml with your respective file names. Further change the config file to your liking.

Create conda environment

conda create -n [Name of your choice] snakemake=8.10.0
conda install graphviz # For visualisation of the DAG (see below)

Activate conda and change working directory

Activate your conda environment with Snakemake and change the working directory to your directory of choice.

conda activate [Name of your snakemake conda]
cd [Path to working directory]

Before running

Make sure you open the interface of Cytoscape. Otherwise, this will lead to errors in the rule rule cytoscape_enrichmentmap. This is done with:

Cytoscape/Cytoscape

Running the snakemake

Change the 4 with the amount of cores you would like to use.

snakemake --resources cytoscape_instances=1 --use-conda -c 4

--resources cytoscape_instances=1 makes sure to only run one Cytoscape rule at a time, because you can not have multiple Cytoscapes open at a time. --use-conda activates the .yaml conda environments for each rule. -n can be added to perform a dry run, to show the rules which are going to be executed.

Creating Directed Acyclic Graphs

Visualisation of the order of the rules in the Snakemake.

snakemake --dag -c 1 | dot -Tsvg > dag.svg

# Use the command below for a simplified DAG
snakemake --rulegraph -c 1 | dot -Tsvg > rulegraph.svg