pandoc-plot 1.3.0 manual

## A Pandoc filter to generate figures from code blocks in documents

`pandoc-plot` turns code blocks present in your documents (Markdown, LaTeX, etc.) into embedded figures, using your plotting toolkit of choice, including Matplotlib, ggplot2, MATLAB, Mathematica, and more.

- Features Overview
  - Captions
  - Link to source code
  - Preamble scripts
  - Support for interactive plots
  - Performance
  - Compatibility with pandoc-crossref
- Detailed usage
  - As a filter
  - Syntax
    - Markdown
    - LaTeX
  - Parameters and options
    - Code highlighting
  - Interactive HTML figures
  - Configuration
    - Executables
    - Command-line arguments
    - Toolkit-specific options
    - Logging
    - Strict mode
  - Other commands
    - Finding installed toolkits
    - Cleaning output
    - Configuration template
  - As a Haskell library
    - Usage with Hakyll
- Warning

## Features Overview

### Captions

You can also specify a caption for your image. This is done using the optional `caption` parameter.

Markdown:

    ```{.matlabplot caption="This is a simple figure with a **Markdown** caption"}
    x  = 0: .1 : 2*pi;
    y1 = cos(x);
    y2 = sin(x);

    figure
    plot(x, y1, 'b', x, y2, 'r-.', 'LineWidth', 2)
    ```

LaTex:

    \begin{minted}[caption=This is a simple figure with a caption]{matlabplot}
    x  = 0: .1 : 2*pi;
    y1 = cos(x);
    y2 = sin(x);

    figure
    plot(x, y1, 'b', x, y2, 'r-.', 'LineWidth', 2)
    \end{minted}

Caption formatting unfortunately cannot be determined automatically. To specify a caption format (e.g. “markdown”, “LaTeX”, etc.), see Configuration.

### Link to source code

In case of an output format that supports links (e.g. HTML), the embedded image generated by `pandoc-plot` can show a link to the source code which was used to generate the file. Therefore, other people can see what code was used to create your figures.

You can turn this on via the `source=true` key:

Markdown:

    ```{.mathplot source=true}
    ...
    ```

LaTex:

    \begin{minted}[source=true]{mathplot}
    ...
    \end{minted}

or via a configuration file.

### Preamble scripts

If you find yourself always repeating some steps, inclusion of scripts is possible using the `preamble` parameter. For example, if you want all Matplotlib plots to have the `ggplot` style, you can write a very short preamble `style.py` like so:

    import matplotlib.pyplot as plt
    plt.style.use('ggplot')

and include it in your document as follows:

    ```{.matplotlib preamble=style.py}
    plt.figure()
    plt.plot([0,1,2,3,4], [1,2,3,4,5])
    plt.title('This is an example figure')
    ```

Which is equivalent to writing the following markdown:

    ```{.matplotlib}
    import matplotlib.pyplot as plt
    plt.style.use('ggplot')

    plt.figure()
    plt.plot([0,1,2,3,4], [1,2,3,4,5])
    plt.title('This is an example figure')
    ```

The equivalent LaTeX usage is as follows:

    \begin{minted}[include=style.py]{matplotlib}

    \end{minted}

This `preamble` parameter is perfect for longer documents with many plots. Simply define the style you want in a separate script! You can also import packages this way, or define functions you often use.

### Support for interactive plots

Starting with version 0.8.0.0, `pandoc-plot` supports the creation of interactive plots (if a toolkit supports it). All you need to do is set the save format to `html`. The resulting plot is fully self-contained, so it can be displayed offline.

### Performance

`pandoc-plot` minimizes work, only generating figures if it absolutely must, i.e. if the content has changed. `pandoc-plot` will save the hash of the source code used to generate a figure in its filename. Before generating a figure, `pandoc-plot` will check it this figure already exists based on the hash of its source! This also means that there is no way to directly name figures.

Moreover, starting with version 0.5.0.0, `pandoc-plot` takes advantage of multicore CPUs, rendering figures in parallel.

Therefore, you can confidently run the filter on very large documents containing hundreds of figures, like a book or a thesis.

### Compatibility with pandoc-crossref

`pandoc-crossref` is a pandoc filter that makes it effortless to cross-reference objects in Markdown documents.

You can use `pandoc-crossref` in conjunction with `pandoc-plot` for the ultimate figure-making pipeline. You can combine both in a figure like so:

    ```{#fig:myexample .plotly_python caption="This is a caption"}
    # Insert figure script here
    ```

    As you can see in @fig:myexample, ...

If the above source is located in file `myfile.md`, you can render the figure and references by applying `pandoc-plot` first, and then `pandoc-crossref`. For example:

    pandoc --filter pandoc-plot --filter pandoc-crossref -i myfile.md -o myfile.html

## Detailed usage

`pandoc-plot` is a command line executable with a few functions. You can take a look at the help using the `-h`/`--help` flag:

    pandoc-plot 1.3.0 - generate figures directly in documents

    Usage: pandoc-plot.EXE [(-v|--version) | --full-version | (-m|--manual)]
                           [COMMAND] [AST]
      This pandoc filter generates plots from code blocks using a multitude of
      possible renderers. This allows to keep documentation and figures in perfect
      synchronicity.

    Available options:
      -v,--version             Show version number and exit.
      --full-version           Show full version information and exit.
      -m,--manual              Open the manual page in the default web browser and
                               exit.
      -h,--help                Show this help text

    Available commands:
      toolkits                 Show information on toolkits and exit.
      clean                    Clean output directories where figures from FILE and
                               log files might be stored. WARNING: All files in
                               those directories will be deleted.
      write-example-config     Write example configuration to a file and exit.

    More information can be found via the manual (pandoc-plot --manual) or the
    repository README, located at https://github.com/LaurentRDC/pandoc-plot

### As a filter

The most common use for `pandoc-plot` is as a pandoc filter, in which case it should be called without arguments. For example:

    pandoc --filter pandoc-plot -i input.md -o output.html

If `pandoc-plot` fails to render a code block into a figure, the filtering will not stop. Your code blocks will stay unchanged, unless you activate strict mode.

You can chain other filters with it (e.g., `pandoc-crossref`) like so:

    pandoc --filter pandoc-plot --filter pandoc-crossref -i input.md -o output.html

### Syntax

The syntax for code blocks in documents is shown below. `pandoc-plot` looks for code blocks with a specific class, depending on the toolkit you want to use. `pandoc-plot` will run the code and capture the figure output. There can only be one figure per code block.

The possible parameters and options are described in further below.

#### Markdown

      ```{.cls param1=value1 param2=value2 ...}
      # script content
      ```

#### LaTeX

Note that the `minted` LaTeX package need not be installed.

    \begin{minted}[param1=value1, param2=value2, ...]{cls}
    ...
    \end{minted}

### Parameters and options

There are parameters that affect the figure that will be included in your document. Here are all the possible general parameters, in Markdown syntax:

      ```{.cls
          .language
          directory=(path)
          caption=(text)
          format=(PNG|PDF|SVG|JPG|EPS|GIF|TIF|WEBP|HTML|LATEX)
          source=(true|True|false|False)
          source_label=(text)
          preamble=(path)
          dpi=(integer)
          dependencies=[...]
          file=(path)
          executable=(path)
          caption_format=(text)
          }
      # script content
      ```

- `cls` must be one of the following: `matplotlib`, `matlabplot`, `plotly_python`, `plotly_r`, `mathplot`, `octaveplot`, `ggplot2`, `gnuplot`, `graphviz`, `bokeh`, `plotsjl`, `plantuml` (new in version 1.1.0).

All following parameters are optional, with their default values controlled by the configuration.

- `language` specifies the programming language used in this block. This parameter is ignored by `pandoc-plot`, but your text editor may use it to highlight code. See Code highlighting below.
- `directory` is a path to the directory where the figure and source code will be saved. You cannot control the file name. This path is either absolute, or relative from the working directory where you call `pandoc-plot`.
- `caption` is the caption text. The format of the caption is specified in the `caption_format` parameter, described below.
- `format` is the desired filetype for the resulting figure. Possible values for `format` are [`PNG`, `PDF`, `SVG`, `JPG`, `EPS`, `GIF`, `TIF`, `WEBP`, `HTML`, `LATEX`]. Not all toolkits support all formats. See `pandoc-plot toolkits` for toolkit-specific information regarding save formats. The `HTML` format is special; it can produce standalone, offline, interactive plots. As such, it only makes sense to use this format when creating HTML documents. Similarly, the `LATEX` format is special; plots in the LaTeX format will be embedded in the document. Therefore, it only makes sense to use this format when creating LaTeX documents.
- `source` is a boolean toggle that determines whether the source code should be linked in the caption or not. Possible values are [`true`, `True`, `false`, `False`].
- `source_label` is the text that links to source code (if `source=true`). This is useful if you are writing text in a different language. The default is `source_label="Source Code"`. You might want to set this via the configuration instead.
- `preamble` is a path to a script that will be included as a preamble to the content of the code block. This path is either absolute, or relative from the working directory where you call `pandoc-plot`.
- `dpi` is the pixel density of the figure in dots-per-inch. Possible values are positive integers. Not all toolkits respect this.
- `dependencies` is a list of files/directories that affect the figure, for example data files. If one of those files/directories changes, `pandoc-plot` will re-render the associated figure. Format is a comma-separated list, e.g. `dependencies=[data.txt, foo.bar, ~/wtv]`. Values for `dependencies` in the configuration file will be appended to the values in a code block.
- `file` is a path to a file from which to read the figure content. If this parameter is used, the content of the code block is ignored. By using this parameter, you can use all the standard tooling of your plotting toolkit of choice, which is especially useful for complex figures.
- `executable` is a path to the executable to use (e.g. `C:\\python3.exe`) or the name of the executable (e.g. `python3`).
- `caption_format` is the text format of the caption. Possible values are exactly the same as `pandoc`’s format specification, usually `FORMAT+EXTENSION-EXTENSION`. For example, captions in Markdown with raw LaTeX would be parsed correctly provided that `caption_format=markdown+raw_tex`. See Pandoc’s guide on Specifying formats.

#### Code highlighting

If your editor supports code highlighting in code blocks, you can also include the programming language. In Markdown:

      ```{.language .cls (options)}
      # script content
      ```

or Latex:

      \begin{minted}[(options)]{language, cls}
      # script content
      \end{minted}

For example, for GGPlot2 figures:

      ```{.r .ggplot2 caption=Highlighted code block}
      # script content
      ```

or (Latex):

      \begin{minted}[caption=Highlighted code block]{r, ggplot2}
      # script content
      \end{minted}

This way, you benefit from code highlighting and `pandoc-plot`.

### Interactive HTML figures

Interactive HTML figures are available for a few toolkits, e.g. `bokeh`. To make a figure interactive, use the output format `format=html`. This only makes sense if your output file is also HTML.

You can take a look at the demonstration page for an example result.

Many interactive plots rely on javascript scripts stored on the internet. If you want to have a self-contained document that can be viewed offline – or you want your document to work for the next 10 years –, you can use pandoc’s `--self-contained` flag:

    pandoc --self-contained --filter pandoc-plot -i mydoc.md -o webpage.html

The resulting output `webpage.html` will contain everything, at the cost of size.

### Configuration

To avoid repetition, `pandoc-plot` can be configured using simple YAML files. Here are all the possible parameters:

    # This is an example configuration. Everything in this file is optional.
    # Please refer to the documentation to know about the parameters herein.
    #
    # The `executable` parameter for all toolkits can be either the
    # executable name (if it is present on the PATH), or
    # the full path to the executable.
    # E.g.:
    #  executable: python3
    #  executable: "C:\Python37\Scripts\python.exe"

    # The following parameters affect all toolkits
    # Directory where to save the plots. The path can be relative to pandoc-plot's
    # current working directory, or absolute.
    directory: plots/

    # Whether or not to include a link to the source script in the caption.
    # Particularly useful for HTML output.
    source: false

    # When `strict: false`, pandoc-plot will leave code blocks untouched if a plot
    # could not be generated. This could happen if, for example, a toolkit is not
    # installed. If you want pandoc-plot to fail instead, use `strict: true`.
    strict: false

    # Text label for links to source code.
    # You can change this label if you are writing a document in a non-English language.
    # This only matters if `source` is set to `true`.
    source_label: Source code

    # Default density of figures in dots per inches (DPI).
    # This can be changed in the document specifically as well.
    dpi: 80

    # Default format in which to save the figures. This can be specified
    # individually as well.
    format: PNG

    # Default files/directories on which all figures depend. If any of these files/directories
    # changes, all figures will be re-rendered.
    # Dependencies specified in code blocks will be appended to this list.
    dependencies:
      - file1.txt
      - file2.txt

    # Text format for the captions. Unfortunately, there is no way to detect
    # this automatically. You can use the same notation as Pandoc's --from
    # parameter, specified here:
    #     https://pandoc.org/MANUAL.html#option--from
    # Example: markdown, rst+raw_tex
    caption_format: markdown+tex_math_dollars

    # Logging configuration
    logging:
      # Possible verbosity values: debug, error, warning, info, silent
      verbosity: warning
      # If the filepath below is not present, then pandoc-plot will log to stderr
      # Otherwise, log messages will be appended to the filepath.
      # filepath: path/to/file.txt

    # The possible parameters for the Matplotlib toolkit
    matplotlib:
      # preamble: matplotlib.py
      tight_bbox: false
      transparent: false
      executable: python
      command_line_arguments:

    # The possible parameters for the MATLAB toolkit
    matlabplot:
      # preamble: matlab.m
      executable: matlab
      command_line_arguments:

    # The possible parameters for the Plotly/Python toolkit
    plotly_python:
      # preamble: plotly-python.py
      executable: python
      command_line_arguments:

    # The possible parameters for the Plotly/R toolkit
    plotly_r:
      # preamble: plotly-r.r
      executable: Rscript
      command_line_arguments:

    # The possible parameters for the Mathematica toolkit
    mathplot:
      # preamble: mathematica.m
      executable: math
      command_line_arguments:

    # The possible parameters for the GNU Octave toolkit
    octaveplot:
      # preamble: octave.m
      executable: octave
      command_line_arguments:

    # The possible parameters for the ggplot2 toolkit
    ggplot2:
      # preamble: ggplot2.r
      executable: Rscript
      command_line_arguments:

    # The possible parameters for the gnuplot toolkit
    gnuplot:
      # preamble: gnuplot.gp
      executable: gnuplot
      command_line_arguments:

    # The possible parameters for the graphviz toolkit
    graphviz:
      # preamble: graphviz.dot
      executable: dot
      command_line_arguments:

    bokeh:
      # preamble: bokeh.py
      executable: python
      command_line_arguments:

    plotsjl:
      # preamble: plotsjl.jl
      executable: julia
      command_line_arguments:

    plantuml:
      # preamble: plantuml.txt
      executable: java
      command_line_arguments: -jar plantuml.jar
      # On Linux, if you have `plantuml.jar` as an executable, you can also
      # use the following configuration instead:
      # plantuml:
      #   executable: plantuml
      #   command_line_arguments:

A file like the above sets the default values; you can still override them in documents directly.

The easiest way to specify configuration for `pandoc-plot` is to place a `.pandoc-plot.yml` file in the current working directory. You can also specify a configuration file in document metadata, under the `plot-configuration` key. For example, in Markdown:

    ---
    title: My document
    author: John Doe
    plot-configuration: /path/to/file.yml
    ---

or on the command line, using the pandoc `-M/--metadata` flag:

    pandoc --filter pandoc-plot -M plot-configuration=/path/to/file.yml ...

The hierarchy of configuration files is as follows:

1. A configuration file specified in the metadata under the `plot-configuration` key;
2. Otherwise, a file in the current working directory named `.pandoc-plot.yml`;
3. Finally, the default configuration is used.

#### Executables

The `executable` parameter for all toolkits can be either the executable name (if it is present on the PATH), or the full path to the executable.

Examples:

    matplotlib:
      executable: python3

    matlabplot:
      executable: "C:\Program Files\Matlab\R2019b\bin\matlab.exe"

#### Command-line arguments

New in version 1.0.2.0

The `command_line_arguments` parameter available for all toolkits provides a way to customize the way interpreters are run. For example, if you want to run the `matplotlib` toolkit with all warnings shown:

    # The possible parameters for the Matplotlib toolkit
    matplotlib:
      executable: python
      command_line_arguments: -Wa

Or if you want `julia` to use more than one thread:

    # The possible parameters for the Matplotlib toolkit
    plotsjl:
      executable: julia
      command_line_arguments: --threads auto

#### Toolkit-specific options

##### Matplotlib

- `tight_bbox` is a boolean that determines whether to use `bbox_inches="tight"` or not when saving Matplotlib figures. For example, `tight_bbox: true`. See here for details.
- `transparent` is a boolean that determines whether to make Matplotlib figure background transparent or not. This is useful, for example, for displaying a plot on top of a colored background on a web page. High-resolution figures are not affected. For example, `transparent: true`.

#### Logging

If you are running `pandoc-plot` on a large document, you might want to turn on logging. You can do so via the configuration file as follows:

    logging:
        # Possible verbosity values: debug, error, warning, info, silent
        # debug level shows all messages
        # error level shows all but debug messages, etc.
        verbosity: info

        # OPTIONAL: log to file
        # Remove line below to log to stderr
        filepath: log.txt

By default, `pandoc-plot` logs warnings and errors to the standard error stream only.

#### Strict mode

New in version 1.0.2.0

By default, `pandoc-plot` leaves code blocks unchanged if a figure fails to be rendered. This might be the case if a plotting toolkit is not installed, or if running the code to render a figure returns an error. In strict mode, `pandoc-plot` will immediately halt if it encounters a problem. You can activate strict mode via configuration:

    strict: true

Strict mode is ideal if you want to ensure that the figures are correctly rendered in the document.

### Other commands

#### Finding installed toolkits

You can determine which toolkits are available on your current machine using the `pandoc-plot toolkits` command. Here is the full help text:

    Usage: pandoc-plot.EXE toolkits [--config PATH]
      Show information on toolkits and exit.

    Available options:
      --config PATH            Path to optional configuration file.
      -h,--help                Show this help text

#### Cleaning output

Figures produced by `pandoc-plot` can be placed in a few different locations. You can set a default location in the Configuration, but you can also re-direct specific figures in other directories if you use the `directory=...` argument in code blocks. These figures will build up over time. You can use the `clean` command to scan documents and delete the associated `pandoc-plot` output files. For example, to delete the figures generated from the `input.md` file:

    pandoc-plot clean input.md

This sill remove all directories where a figure could have been placed. WARNING: all files will be removed.

Here is the full help text for the `clean` command:

    Usage: pandoc-plot.EXE clean [--config PATH] FILE
      Clean output directories where figures from FILE and log files might be
      stored. WARNING: All files in those directories will be deleted.

    Available options:
      --config PATH            Path to optional configuration file.
      -h,--help                Show this help text

#### Configuration template

Because `pandoc-plot` supports a few toolkits, there are a lot of configuration options. Don’t start from scratch! The `write-example-config` command will create a file for you, which you can then modify:

    pandoc-plot write-example-config

You will need to re-name the file to `.pandoc-ploy.yml` to be able to use it, so don’t worry about overwriting your own configuration.

Here is the full help text for the `write-example-config` command:

    Usage: pandoc-plot.EXE write-example-config [--path FILE]
      Write example configuration to a file and exit.

    Available options:
      --path FILE              Target location of the configuration file. Default is
                               ".example-pandoc-plot.yml"
      -h,--help                Show this help text

### As a Haskell library

To include the functionality of `pandoc-plot` in a Haskell package, you can use the `make` function (for single blocks) or `plotFilter` function (for entire documents). Take a look at the documentation on Hackage.

#### Usage with Hakyll

In case you want to use the filter with your own Hakyll setup, you can use a transform function that works on entire documents:

    import Text.Pandoc.Filter.Plot (plotFilter, defaultConfiguration)
    import Text.Pandoc.Definition (Pandoc, Format(..)) -- from pandoc-types
    import Hakyll

    plotFilter' :: Pandoc -> IO Pandoc
    plotFilter' =
      -- Notify pandoc-plot that the final conversion will be to HTML
      -- This helps give better error messages and adjust default values
      plotFilter defaultConfiguration (Just $ Format "html5")

    -- Unsafe compiler is required because of the interaction
    -- in IO (i.e. running an external script).
    makePlotPandocCompiler :: Compiler (Item String)
    makePlotPandocCompiler =
      pandocCompilerWithTransformM
        defaultHakyllReaderOptions
        defaultHakyllWriterOptions
        (unsafeCompiler . plotFilter')

## Warning

Do not run this filter on unknown documents. There is nothing in `pandoc-plot` that can stop a script from performing evil actions.