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 Specifying options.
Input and output logistics¶
- treefile
- Name of file containing tree and tip states. See Input tree file.
- optfile
- Name of file containing formatting options. See Specifying 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 Note on RGB colors
[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 Note on RGB colors [default is black]
- backcolor
Color of the image background.
= "(R, G, B)" see Note on RGB colors [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 Note on RGB colors [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]
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.