Standalone executable

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/executable.zip
unzip executable.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.

./funky_heatmap --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:

./funky_heatmap --data funky_heatmap/example_data.tsv --output plot.pdf

ℹ Could not find column 'id' in data. Using rownames as 'id'.
ℹ No column info was provided, assuming all columns in `data` are to be plotted.
ℹ Column info did not contain column `name`, using `id` to generate it.
ℹ Column info did not contain information on which columns to plot, inferring from `data` types.
ℹ Column info did not contain group information, assuming columns are ungrouped.
ℹ Column info did not contain a column called 'palette', generating palettes based on the 'geom' column.
ℹ Column info did not contain a column called 'options', generating ptions based on the 'geom' column.
ℹ No row info was provided, assuming all rows in `data` are to be plotted.
ℹ Row info did not contain group information, assuming rows are ungrouped.
ℹ No palettes were provided, trying to automatically assign palettes.
ℹ Palette named 'numerical_palette' was not defined. Assuming palette is numerical. Automatically selected palette 'Blues'.

More information

See the funkyheatmap home page for more information and documentation.