.. _options: ******************* List of All Options ******************* Recall that option names must be preceded with ``--`` when used on the command line. Alternatively, they can be placed in a file whose first line is ``[pietree]``. See :ref:`usage-options`. Input and output logistics -------------------------- ``treefile`` Name of file containing tree and tip states. See :ref:`usage-treefile`. ``optfile`` Name of file containing formatting options. See :ref:`usage-options`. ``outfile`` Name for the output file. If it doesn’t have a suffix (like ``.pdf``), an appropriate one will be appended. [default is ``pietree``] ``outformat`` File format of the output image. If an ``outfile`` with a suffix is also specified, ``outformat`` takes precedence and an appropriate suffix will be appended. ``= pdf`` Adobe’s format [the default] ``= eps`` (encapsulated) postscript ``= svg`` scalable vector graphics (works with Inkscape and Illustrator) ``= png`` portable network graphics (lossless bitmap) ``width`` Width of the canvas. The image is scaled horizontally to match this width. ``=`` any positive number [default is 800] ``height`` Height of the canvas. Doesn't affect scaling of the image. ``=`` any positive number [default is determined by tree size for ``shape = rect`` or is ``width`` for ``shape = radial``] ``xmargin`` Margin size on the left and right of the image. For ``shape = radial``, these are based on the longest tip name. ``=`` any positive number [default is 20] ``ymargin`` Margin size on the top and bottom of the image. ``=`` any positive number [default is 10] Graphical elements ------------------ ``shape`` Shape in which the tree is drawn. ``= rect`` rectangular, with all the tips on the right [the default] ``= radial`` radial, with the tips along the outside of a circle ``scalebar`` Draw a bar showing the time scale of the plot. ``= no`` no scale bar is drawn [the default] ``= yes`` a scale bar of some auto-calculated length is drawn ``= X`` a scale bar of length ``X`` is drawn (replace ``X`` with a number, obviously) ``colorX`` Color representing state ``X``. Replace ``X`` with ``0``, ``1``, etc. ``= "(R, G, B)"`` see :ref:`colornote` [defaults: ``color0 = "(1, 1, 1)"`` (white), ``color1 = "(0, 0, 0)"`` (black), no defaults for additional states] ``pieradius`` Radius of the pie chart showing the node reconstruction. ``=`` any positive number [default is 7] ``boxsize`` Height of the box showing the tip state. ``=`` any positive number [default is 1.9 * ``pieradius``] ``rimthick`` Thickness of the lines around the pies and boxes. ``=`` any positive number [default is 2] ``linethick`` Thickness of the branch lines. ``=`` any positive number [default is 1] ``linecolor`` Color of the branches of the tree and other lines. ``= "(R, G, B)"`` see :ref:`colornote` [default is black] ``backcolor`` Color of the image background. ``= "(R, G, B)"`` see :ref:`colornote` [default is transparent for ``outformat = png``, white otherwise] ``tipspacing`` Space between tip markers. ``=`` any positive number [default is 1.5 * ``boxsize``] Text formatting --------------- ``tipnamesize`` Font size of the tip labels. ``=`` any positive number [default is ``boxsize``] ``nodenamesize`` Font size of the internal node labels. ``=`` any positive number [default is 0.75 * ``tipnamesize``] ``italic`` Whether to italicize the text ``= yes`` italics ``= no`` normal upright [the default] ``serif`` Whether to use a serif font. ``= yes`` serif font ``= no`` sans-serif font [the default] ``underscorespace`` Whether to replace ``_`` with a space in tip and node names. ``= yes`` do replace underscores ``= no`` don't replace underscores [the default] ``textcolor`` Color of tip and node labels ``= "(R, G, B)"`` see :ref:`colornote` [default is black] ``tipnamestatecolor`` Whether to color the tip text label according to the tip state. ``= yes`` take tip label color from tip state ``= no`` use ``textcolor`` for tip label [the default] .. _colornote: Note on RGB colors ------------------ ``R``, ``G``, and ``B`` are the values for the red, green, and blue components of the color. Each takes a value between 0 and 1. These three numbers must be separated with commas and the whole thing surrounded with parentheses. On the command line, put quote marks outside the parentheses. For example, ``color0 = (0.24, 0.62, 0.82)`` in an option file, and ``--color0 = "(0.24, 0.62, 0.82)"`` on the command line.