| 1 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"> |
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| 2 | <HTML> |
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| 3 | <HEAD> |
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| 4 | <TITLE>drawgram</TITLE> |
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| 5 | <META NAME="description" CONTENT="drawgram"> |
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| 6 | <META NAME="keywords" CONTENT="drawgram"> |
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| 7 | <META NAME="resource-type" CONTENT="document"> |
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| 10 | </HEAD> |
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| 11 | <BODY BGCOLOR="#ccffff"> |
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| 12 | <DIV ALIGN=RIGHT> |
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| 13 | version 3.6 |
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| 14 | </DIV> |
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| 15 | <P> |
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| 16 | <DIV ALIGN=CENTER> |
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| 17 | <H1>DRAWGRAM</H1> |
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| 18 | </DIV> |
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| 19 | <P> |
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| 20 | © Copyright 1990-2002 by The University of |
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| 21 | Washington. Written by Joseph Felsenstein. Permission is granted to copy |
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| 22 | this document provided that no fee is charged for it and that this copyright |
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| 23 | notice is not removed. |
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| 24 | <P> |
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| 25 | DRAWGRAM interactively plots a cladogram- or phenogram-like rooted tree |
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| 26 | diagram, with many options including orientation of tree and branches, |
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| 27 | style of tree, label sizes and angles, tree depth, margin sizes, stem |
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| 28 | lengths, and placement of nodes in the tree. Particularly if you can |
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| 29 | use your computer to preview the plot, you can very |
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| 30 | effectively adjust the details of the plotting to get just the kind of |
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| 31 | plot you want. |
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| 32 | <P> |
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| 33 | To understand the working of DRAWGRAM and DRAWTREE, you should first |
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| 34 | read the <A HREF="draw.html">Tree Drawing Programs web page</A> |
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| 35 | in this documentation. |
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| 36 | <P> |
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| 37 | As with DRAWTREE, to run DRAWGRAM you need a compiled copy of the |
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| 38 | program, a font file, and a tree file. The tree file has a default name |
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| 39 | of <TT>intree</TT>. The font file has a default name of "fontfile". If there is |
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| 40 | no file of that name, the program will ask you for the name of a font file |
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| 41 | (we provide ones that have the names <TT>font1</TT> through <TT>font6</TT>). |
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| 42 | Once you decide on a favorite one of these, you could make a copy of it |
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| 43 | and call it <TT>fontfile</TT>, and it will then be used by default. |
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| 44 | Note that the program will get confused if the input tree file has the number |
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| 45 | of trees on the first line of the file, so that numbr may have to be removed. |
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| 46 | <P> |
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| 47 | Once these choices have been made you will see the central menu of the |
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| 48 | program, which looks like this: |
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| 49 | <P> |
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| 50 | <TABLE><TR><TD BGCOLOR=white> |
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| 51 | <PRE> |
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| 52 | |
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| 53 | Rooted tree plotting program version 3.6a3 |
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| 54 | |
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| 55 | Here are the settings: |
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| 56 | 0 Screen type (IBM PC, ANSI): (none) |
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| 57 | P Final plotting device: Postscript printer |
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| 58 | V Previewing device: X Windows display |
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| 59 | H Tree grows: Horizontally |
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| 60 | S Tree style: Phenogram |
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| 61 | B Use branch lengths: Yes |
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| 62 | L Angle of labels: 90.0 |
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| 63 | R Scale of branch length: Automatically rescaled |
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| 64 | D Depth/Breadth of tree: 0.53 |
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| 65 | T Stem-length/tree-depth: 0.05 |
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| 66 | C Character ht / tip space: 0.3333 |
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| 67 | A Ancestral nodes: Weighted |
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| 68 | F Font: Times-Roman |
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| 69 | M Horizontal margins: 1.65 cm |
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| 70 | M Vertical margins: 2.16 cm |
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| 71 | # Pages per tree: one page per tree |
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| 72 | |
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| 73 | Y to accept these or type the letter for one to change |
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| 74 | </PRE> |
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| 75 | </TD></TR></TABLE> |
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| 76 | <P> |
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| 77 | These are the settings that control the appearance of the tree, which |
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| 78 | has already been read in. You can either accept these as is, in which |
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| 79 | case you would answer Y to the question and press the Return or Enter |
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| 80 | key, or you can answer N if you want to change one, or simply type the |
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| 81 | character corresponding to the one you want to change (if you answer N it |
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| 82 | will just immediately ask you for that number anyway). |
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| 83 | <P> |
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| 84 | For a first run, particularly if previewing is available, you might accept |
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| 85 | these default values and see what the result looks like. The program |
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| 86 | will then tell you it is about to preview the tree and ask you to press |
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| 87 | Return or Enter when you are ready to see this (you will probably have |
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| 88 | to press it twice). If you are on a Windows system (and have its graphics |
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| 89 | selected as your previewing option), on a Unix or Linux system and are |
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| 90 | using X windows for previewing, or are on a Macintosh system, a new |
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| 91 | window will open with the preview in it. If you are using the Tektronix |
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| 92 | preview option the preview will appear in the window where the menu was. |
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| 93 | <P> |
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| 94 | On X Windows, Macintosh, and Windows you can resize the preview window, |
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| 95 | though for some of these you may have to ask the system to redraw the |
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| 96 | preview to see it at the new window size. |
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| 97 | <P> |
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| 98 | Once you are finished looking at the preview, you will want to |
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| 99 | specify whether the program should make the final plot or change some of |
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| 100 | the settings. This is done differently on the different previews: |
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| 101 | <P> |
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| 102 | <UL> |
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| 103 | <LI>In <B>X Windows</B> you should make the menu window the active |
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| 104 | window. You may need to move the mouse over it, or click in it, or |
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| 105 | click on its top bar. You do not need to try to close the preview |
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| 106 | window yourself, and usually if you do this will cause trouble. |
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| 107 | <LI>In <B>Windows</B> use the <TT>File</TT> menu in the preview window |
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| 108 | and choose either the <TT>Change Parameters</TT> menu item, or if |
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| 109 | you are ready to make the final plot, choose the <TT>Plot</TT> menu item. |
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| 110 | <LI>On a <B>Macintosh</B> system, you can simply use the little box in |
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| 111 | the corner of the preview window to close it. The text window for the |
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| 112 | menu will then be active. |
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| 113 | <LI>In <B>PC graphics</B> press on the Enter key. The screen with the |
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| 114 | preview should disappear and the settings menu reappear. |
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| 115 | <LI>With a <B>Tektronix</B> preview, you may need to change your screen |
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| 116 | from a Tektronix-compatible mode to see the menu again. |
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| 117 | </UL> |
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| 118 | <P> |
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| 119 | Except with the Macintosh preview, the program will |
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| 120 | now ask you if the tree is now ready to be plotted. If you answer Y (for |
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| 121 | Yes) (or choose this option in the <TT>File</TT> menu of the preview |
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| 122 | window in the case of Windows) the program will usually write a plot file |
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| 123 | (with some plot options it will draw the tree on the screen). Then it will |
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| 124 | terminate. |
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| 125 | <P> |
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| 126 | But if you do not say that you are ready to plot the tree, |
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| 127 | it will go back to the above menu, allow |
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| 128 | you to change more options, and go through the whole process again. The |
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| 129 | easiest way to learn the meaning of the options is to try them, |
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| 130 | particularly if previewing is available. Below I will describe them one |
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| 131 | by one; you may prefer to skip reading this unless you are puzzled about |
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| 132 | one of them. |
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| 133 | <P> |
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| 134 | <H2>THE OPTIONS</H2> |
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| 135 | <P> |
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| 136 | <DL COMPACT> |
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| 137 | <DT>O</DT> <DD>This is an option that allows you to change the menu window |
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| 138 | to be an ANSI terminal or an IBM PC terminal. Generally you will not |
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| 139 | want to change this.</DD> |
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| 140 | <P> |
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| 141 | <DT>P</DT> <DD>This allows you to choose the Plotting device or file |
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| 142 | format. We have discussed the possible choices in the |
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| 143 | <A HREF="draw.html">draw programs documentation web page</A>.</DD> |
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| 144 | <P> |
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| 145 | <DT>V</DT> <DD>This allows you to change the type of preView window (or |
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| 146 | even turn off previewing. We have discussed the different possible |
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| 147 | choices in the <A HREF="draw.html">draw programs documentation web page</A>.</DD> |
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| 148 | <P> |
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| 149 | <DT>H</DT> <DD>Whether the tree grows Horizontally or |
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| 150 | vertically. The horizontal growth will be from left to right. This |
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| 151 | option is self explanatory. The other options are designed so that when |
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| 152 | we switch this direction of growth the tree still looks the same, except |
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| 153 | for orientation and overall size. This option is toggled, that is, |
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| 154 | when it is chosen the orientation changes, going back and forth between |
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| 155 | Vertical and Horizontal. The default orientation is Horizontal.</DD> |
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| 156 | <P> |
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| 157 | <DT>S</DT> <DD>The Style of the tree. There are six |
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| 158 | styles possible: Cladogram, Phenogram, Curvogram, Eurogram, Swoopogram, |
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| 159 | and Circular Tree. These are chosen by the letters C, P, V, E, S and O. |
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| 160 | These take a little explaining. |
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| 161 | <P> |
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| 162 | In spite of the words "cladogram" and "phenogram", there is no |
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| 163 | implication of the extent to which you consider these diagrams as being |
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| 164 | genealogies or phenetic clustering diagrams. The names refer to pictorial |
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| 165 | style, not your own intended final use for the diagram. The six styles |
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| 166 | can be described as follows (assuming a vertically growing tree): |
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| 167 | <P> |
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| 168 | <DL> |
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| 169 | <DT>Cladogram</DT> <DD>nodes are connected to other nodes and to tips by straight |
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| 170 | lines going directly from one to the other. This gives a V-shaped |
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| 171 | appearance. The default settings if there are no branch lengths are |
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| 172 | designed to yield a V-shaped tree with a 90-degree angle at the base.</DD> |
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| 173 | <P> |
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| 174 | <DT>Phenogram</DT> <DD>nodes are connected to other nodes and to other tips by |
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| 175 | a horizontal and then a vertical line. This gives a particularly |
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| 176 | precise idea of horizontal levels.</DD> |
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| 177 | <P> |
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| 178 | <DT>Curvogram</DT> <DD>nodes are connected to other nodes and to tips by a curve |
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| 179 | which is one fourth of an ellipse, starting out horizontally and then |
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| 180 | curving upwards to become vertical. This pattern was suggested by |
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| 181 | Joan Rudd.</DD> |
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| 182 | <P> |
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| 183 | <DT>Eurogram</DT> <DD>so-called because it is a version of cladogram diagram |
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| 184 | popular in Europe. Nodes are |
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| 185 | connected to other nodes and to tips by a diagonal line that goes outwards |
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| 186 | and goes at most one-third of the way up to the next node, then turns |
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| 187 | sharply straight upwards and is vertical. Unfortunately it is nearly |
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| 188 | impossible to guarantee, when branch lengths are used, that the angles |
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| 189 | of divergence of lines are the same.</DD> |
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| 190 | <P> |
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| 191 | <DT>Swoopogram</DT> <DD>this option connects two nodes |
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| 192 | or a node and a tip using two curves that are actually each one-quarter |
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| 193 | of an ellipse. The first part starts out vertical and then bends over |
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| 194 | to become horizontal. The second part, which is at least two-thirds |
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| 195 | of the total, starts out horizontal and then bends up to become |
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| 196 | vertical. The effect is that two lineages split apart gradually, then |
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| 197 | more rapidly, then both turn upwards.</DD> |
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| 198 | <P> |
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| 199 | <DT>Circular Tree</DT> <DD>This is a style introduced by David Swofford |
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| 200 | in PAUP*. The tree grows outward from a central point, being essentially |
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| 201 | a Phenogram style tree in polar coordinates. The tips form a 360-degree |
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| 202 | circle. The "vertical" lines run outward radially from the center, and the |
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| 203 | "horizontal" lines are arcs of circles centered on it.</DD> |
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| 204 | </DL> |
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| 205 | <P> |
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| 206 | You should experiment with these and decide which you want -- it depends |
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| 207 | very much on the effect you want.</DD> |
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| 208 | <P> |
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| 209 | <DT>B</DT> <DD>Whether the tree has Branch lengths that are |
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| 210 | being used in the diagram. If the tree that was read in had a full set |
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| 211 | of branch lengths, it will be assumed as a default that you want to use |
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| 212 | them in the diagram, but you can specify that they are not to be used. If |
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| 213 | the tree does not have a full set of branch lengths then this will |
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| 214 | be indicated, and if you try to use branch lengths the program will |
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| 215 | refuse to allow you to do so. Note that when you change option B, the node |
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| 216 | position option A may change as well.</DD> |
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| 217 | <P> |
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| 218 | <DT>L</DT> <DD>The angle of the Labels. The angle is always |
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| 219 | calculated relative to a vertical tree; whether the tree is horizontal |
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| 220 | or vertical, if the labels are at an angle of 90 degrees they run |
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| 221 | parallel to direction of tree growth. The default value is 90 |
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| 222 | degrees. The option allows you to choose any angle from 0 to 90 degrees.</DD> |
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| 223 | <P> |
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| 224 | <DT>R</DT> <DD>How the branch lengths will be translated |
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| 225 | into distances on the output device. Note that when branch lengths |
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| 226 | have not been provided, there are implicit branch lengths specified |
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| 227 | by the type of tree being drawn. This |
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| 228 | option will toggle back and forth between automatic |
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| 229 | adjustment of branch lengths so that the diagram will just fit into the |
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| 230 | margins, and you specifying how many centimeters there will be per unit |
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| 231 | branch length. This is included so that you can plot different trees |
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| 232 | to a common scale, showing which ones have longer or shorter branches than |
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| 233 | others. Note that if you choose too large a value for centimeters per |
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| 234 | unit branch length, the tree will be so big it will overrun the plotting |
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| 235 | area and may cause failure of the diagram to display properly. Too small |
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| 236 | a value will cause the tree to be a nearly invisible dot.</DD> |
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| 237 | <P> |
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| 238 | <DT>D</DT> <DD>The ratio between the Depth and the |
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| 239 | breadth of the tree. It is initially set near 0.5, to approximate a |
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| 240 | V-shaped tree, but you may want to try a larger value to get a longer |
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| 241 | and narrower tree. Depth and breadth are described as if the tree grew |
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| 242 | vertically, so that depth is always measured from the root to the tips |
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| 243 | (not including the length of the labels).</DD> |
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| 244 | <P> |
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| 245 | <DT>T</DT> <DD>The length of the sTem of the tree |
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| 246 | as a fraction of the depth of the tree. You may want to either lengthen |
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| 247 | the stem or remove it entirely by giving a value of zero.</DD> |
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| 248 | <P> |
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| 249 | <DT>C</DT> <DD>The Character height, measured as a fraction |
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| 250 | of the tip spacing. If the labels are rotated to a shallow |
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| 251 | angle, the character height will be automatically adjusted in hopes of |
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| 252 | avoiding collision of labels at different tips. This option allows you |
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| 253 | to change the size of the labels yourself. On output devices where |
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| 254 | line thicknesses can be varied, the thickness of the tree lines will |
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| 255 | automatically be adjusted to be proportional to the character height, |
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| 256 | which is an additional reason you may want to change character height.</DD> |
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| 257 | <P> |
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| 258 | <DT>A</DT> <DD>Controls the |
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| 259 | positions of the Ancestral (interior) nodes. This can greatly affect the |
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| 260 | appearance of the tree. The vertical positions (these descriptions assume a |
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| 261 | a tree growing vertically) are not under your control except insofar as you |
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| 262 | specify the use or non-use of branch lengths. If you choose to change |
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| 263 | this option you will see the menu: |
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| 264 | <P> |
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| 265 | <TABLE><TR><TD BGCOLOR=white> |
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| 266 | <PRE> |
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| 267 | Should interior node positions: |
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| 268 | be Intermediate between their immediate descendants, |
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| 269 | Weighted average of tip positions |
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| 270 | Centered among their ultimate descendants |
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| 271 | iNnermost of immediate descendants |
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| 272 | or so that tree is V-shaped |
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| 273 | (type I, W, C, N or V): |
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| 274 | </PRE> |
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| 275 | </TD></TR></TABLE> |
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| 276 | <P> |
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| 277 | The five methods (Intermediate, Weighted, Centered, Innermost, and |
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| 278 | V-shaped) are different horizontal positionings of the interior nodes. |
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| 279 | It will be helpful to you to try these out and see which you like best. |
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| 280 | Intermediate places the node halfway between its immediate descendants |
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| 281 | (horizontally), Weighted places it closer to that descendant who is |
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| 282 | closer vertically as well, and Centered centers the node below the |
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| 283 | horizontal positions of the tips that are descended from that node. You |
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| 284 | may want to choose that option that prevents lines from crossing each |
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| 285 | other. |
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| 286 | <P> |
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| 287 | V-shaped is another option, one designed, if there are no branch lengths |
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| 288 | being used, to yield a v-shaped tree of regular appearance. With branch |
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| 289 | lengths it will not necessarily do so. "Innermost" is the most unusual |
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| 290 | option: it chooses a center for the tree, and always places interior |
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| 291 | nodes below the innermost of their immediate descendants. This leads |
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| 292 | to a tree that has vertical lines in the center, like a tree with a |
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| 293 | trunk. |
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| 294 | <P> |
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| 295 | If the tree you are plotting has a full set of lengths, then when it is |
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| 296 | read in the node position option is automatically set to "intermediate", |
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| 297 | which is the setting with the least likelihood of lines in the tree |
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| 298 | crossing. If it does not have lengths the option is set to "V-shaped". |
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| 299 | If you change option B which tells the program whether to try to use |
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| 300 | the branch lengths, then the node position option will automatically be |
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| 301 | reset to the appropriate one of these defaults. This may be confusing |
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| 302 | if you do not realise that it is happening.</DD> |
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| 303 | <P> |
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| 304 | <DT>F</DT> <DD>Allows you to select the |
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| 305 | name of the Font that you will use for the species names. This is |
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| 306 | allowed for some of the plotter drivers (this menu item does not |
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| 307 | appear for the others). You can |
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| 308 | select the name of any font that is available for your plotter, for |
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| 309 | example "Courier-Bold" or "Helvetica". The label will then be |
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| 310 | printed using that font rather than being drawn line-by-line as it |
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| 311 | is in the default Hershey font. In the preview of the tree, the |
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| 312 | Hershey font is always used (which means that it may look different from |
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| 313 | the final font). The size of the characters in the species names is |
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| 314 | scaled according to the label heights you have selected in the menu, |
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| 315 | whether plotter fonts or the Hershey font are used. Note that for some |
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| 316 | plotter drivers (particular Xfig and PICT) fonts can be used only if the |
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| 317 | species labels are horizontal or vertical (at angles of 0 degrees or |
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| 318 | 90 degrees).</DD> |
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| 319 | <P> |
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| 320 | <DT>M</DT> <DD>The horizontal and vertical Margins in |
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| 321 | centimeters. You can enter new margins (you must enter new values for |
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| 322 | both horizontal and vertical margins, though these need not be different |
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| 323 | from the old values). For the moment I do not allow you to specify left |
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| 324 | and right margins separately, or top and bottom margins separately. In |
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| 325 | a future release I hope to do so.</DD> |
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| 326 | <P> |
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| 327 | <DT>#</DT> <DD>The number of pages per tree. Defaults to one, but if |
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| 328 | you need a physically large tree you may want to choose a larger |
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| 329 | number. For example, to make a big tree for a poster, choose a larger |
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| 330 | number of pages horizontally and vertically (the program will ask you |
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| 331 | for these numbers), get out your scissors and paste or tape, and |
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| 332 | go to work.</DD> |
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| 333 | </DL> |
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| 334 | <P> |
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| 335 | I recommend that you try all of these options (particularly if you can |
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| 336 | preview the trees). It is of particular use to try combinations of the |
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| 337 | style of tree (option S) with the different methods of placing |
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| 338 | interior nodes (option A). You will find that a wide variety of |
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| 339 | effects can be achieved. |
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| 340 | <P> |
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| 341 | I would appreciate suggestions for improvements in DRAWGRAM, but please |
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| 342 | be aware that the source code is already very large and I may not be |
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| 343 | able to implement all suggestions. |
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| 344 | </BODY> |
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| 345 | </HTML> |
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