Nextflow module

funkyheatmap is available as a standalone executable. The data formats are very similar as the underlying R function. Instead of data frames you should pass TSV files and instead of a named list (for the palettes) you should pass a yaml file.

Install

wget https://github.com/funkyheatmap/funkyheatmap/releases/latest/download/nextflow.zip
unzip nextflow.zip -d funky_heatmap

In order for this to work, you need to have Docker and Bash installed (nothing else).

View help

Run --help to get more information on the arguments of funky heatmap.

nextflow run funky_heatmap/main.nf --help

Example

We also processed the mtcars dataset and stored it as a tsv file. To generate a plot with it, use the following commands:

nextflow run funky_heatmap/main.nf \
  --data funky_heatmap/example_data.tsv \
  --output plot.pdf \
  --publish_dir . \
  -profile docker

More information

See the funkyheatmap home page for more information and documentation.