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executable.qmd
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executable.qmd
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---
title: "Standalone executable"
vignette: >
%\VignetteIndexEntry{Standalone executable}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{quarto::html}
editor_options:
chunk_output_type: console
---
`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
```bash
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.
```bash
./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:
```bash
./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](https://funkyheatmap.github.io/funkyheatmap/) for more information and documentation.