plotsettings 1.0.1

Easily format figures to match the publication requirements of an academic journal

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Highlights

Tearing your hair out trying to make your figures conform to the author guidelines for a particular journal? Got rejected from PNAS and can’t bring yourself to change all the fonts for submission to PLOS ONE? Let plotsettings make it easy for you! plotsettings is a convenient way of making sure your figures fit the requirements for publication. One line is sufficient to choose a target journal, and just one more line to automatically output figures that fit cleanly into 1, 2 or even 1.5 columns! You can even set the aspect ratio of your figure and be warned if your figure gets taller than the height of one page. In fact, plotsettings already knows the appropriate font, text size, and figure dimensions for all of these journals:

• Proceedings of the Royal Society B (use argument ‘ProcRoySocB’)

• Public Library of Science One (use argument ‘PLOSONE’)

• Deep Sea Research II (use argument ‘DSRII’)

• Marine Ecology Progress Series (use argument ‘MEPS’)

• Journal of Experimental Biology (use argument ‘JEB’)

• Proceedings of the National Academy of Sciences, USA (use argument ‘PNAS’)

• Ecology Letters (use argument ‘EcolLett’)

• Presentation (okay, this is not a journal but it’s still useful for outputting figures to presentation slides; access with the argument ‘Presentation’)

Don’t see the journal you want on the list (say you want to publish in the Proceedings of the 6th ACM Workshop on Next Generation Mobile Computing for Dynamic Personalised Travel Planning)? Compile your own list of journals by creating a python file containing a single dictionary with settings for every journal you use! You can specify any parameters that are accepted by matplotlib.rcParams as well as the column width, gutter width and page height.

Also, as a Bonus:

• 1-line labeling of all the subplots in a figure (e.g. with ‘(a)’, ‘(b)’, ‘(c)’ etc.) using the function panel_labels!

Installation

plotsettings has only been tested in Python 2.7

Install through pip:

$ pip install plotsettings

Requires the following non-standard libraries:

• matplotlib

Usage

First set the journal you want to submit to:

publishable = plotsettings.Set('MEPS') # Lets publish in Marine Ecology Progress Series!

Then set the dimensions of a particular figure with the line:

publishable.set_figsize(n_columns = 1, n_rows = 1)

This will cause the next figure that is drawn to be 1 column wide (81 mm for MEPS) x 1 row high (the concept of ‘rows’ is a little made up, but the default is that one row is equal to one column width multiplied by the golden ratio, so in this case 50.1 mm). Once the first figure is drawn, we can set the next figure to be 2 columns wide and 1 row tall and this time set the row height to be equal to the column width like this:

publishable.set_figsize(2, 1, aspect_ratio = 1)

Importantly, plotsettings doesn’t just calculate the width of a 2-column figure as two times the width of one column, but includes the width of the gutter (the space between columns on a page) as well. Therefore, the figure that follows the above line will end up being 169 mm wide (2 columns of 81 mm each plus a 7 mm gutter) and 81 mm tall (row height = 1*column width).

Once the figure has been created, conveniently add labels to each subplot (if you have a multipart figure):

publishable.panel_labels(fig = None, position = 'outside', case = 'lowercase',
                                                 prefix = '', suffix = '.', fontweight = 'bold')

to create the labels (‘a.’, ‘b.’, ‘c.’ …) in bold letters outside the top-left corner of each subplot.

Custom journal settings can be used by specifying a python file on the PYTHONPATH:

publishable = plotsettings.Set('my_journal_name', 'module_name')

The file ‘module_name’ should contain a single dictionary named journals with the following structure:

journals = {'some_journal': {'key1': value, 'key2': value},
            'another_journal': {'key1': value, 'key2': value}}

where ‘some_journal’ is the identifying name of an academic journal (e.g. ‘Nature’) and ‘key1’, ‘key2’ correspond either to valid keys for matplotlib.rcParams (for example the font name and size) or to one of ‘column_width’, ‘gutter_width’, ‘max_height’ or ‘units’. Each of these non-rcParams keys except for ‘max_height’ is required. For an example of this kind of dictionary, see the module ‘journals’ in this package. Definitions of valid keys to rcParams can be found here. The non-rcParams keys are:

• column_width (required) - the maximum width a figure is allowed to be while still fitting within a single column.

• gutter_width (required) - the width of the gutter (space between columns). This can usually be found by comparing the maximum width that a journal allows for a single- column figure with the maximum width of a 2-column figure. For example, PLOS ONE allows a 1-column figure to be 83 mm in width and a 2-column figure to be 173.5 mm, meaning that the gutter width (173.5 - 83*2) is 7.5 mm wide.

• max_height (optional) - the maximum height a figure is allowed to be while fitting on a single page (i.e. the page height).

• units (required) - the units in which the above are reported. Can be one of ‘mm’, ‘cm’, ‘inch’, or ‘pts’

Version

1.0.1 - Not extensively tested. Please email to let me know of any issues.

Changelog

1.0.1 (OCTOBER/14/2014)

• Fixed bug that made plotsettings.Set unable to find the default journals module

• Added function panel_labels for convenient, 1-line addition of formatted panel labels (e.g. A, B, C) to every subplot in a figure.

• Added ‘Presentation’ as a journal type for PowerPoint slides

1.0.0 (OCTOBER/13/2014)

• First release