EMBOSS: fdrawgram

| fdrawgram

## Wiki

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Please help by correcting and extending the Wiki pages.

## Function

Plots a cladogram- or phenogram-like rooted tree diagram

## Description

Plots rooted phylogenies, cladograms, circular trees and phenograms in a wide variety of user-controllable formats. The program is interactive and allows previewing of the tree on PC, Macintosh, or X Windows screens, or on Tektronix or Digital graphics terminals. Final output can be to a file formatted for one of the drawing programs, for a ray-tracing or VRML browser, or one at can be sent to a laser printer (such as Postscript or PCL-compatible printers), on graphics screens or terminals, on pen plotters or on dot matrix printers capable of graphics.

Similar to DRAWTREE but plots rooted phylogenies.

## Algorithm

DRAWGRAM interactively plots a cladogram- or phenogram-like rooted tree diagram, with many options including orientation of tree and branches, style of tree, label sizes and angles, tree depth, margin sizes, stem lengths, and placement of nodes in the tree. Particularly if you can use your computer to preview the plot, you can very effectively adjust the details of the plotting to get just the kind of plot you want.

To understand the working of DRAWGRAM and DRAWTREE, you should first read the Tree Drawing Programs web page in this documentation.

As with DRAWTREE, to run DRAWGRAM you need a compiled copy of the program, a font file, and a tree file. The tree file has a default name of intree. The font file has a default name of "fontfile". If there is no file of that name, the program will ask you for the name of a font file (we provide ones that have the names font1 through font6). Once you decide on a favorite one of these, you could make a copy of it and call it fontfile, and it will then be used by default. Note that the program will get confused if the input tree file has the number of trees on the first line of the file, so that numbr may have to be removed.

## Usage

Here is a sample session with fdrawgram

    % fdrawgram -previewer n
    Plots a cladogram- or phenogram-like rooted tree diagram
    Phylip tree file: drawgram.tree
    Phylip drawgram output file [drawgram.fdrawgram]:

    DRAWGRAM from PHYLIP version 3.69.650
    Reading tree ...
    Tree has been read.
    Loading the font ....
    Font loaded.

    Writing plot file ...

    Plot written to file "drawgram.fdrawgram"

    Done.

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Plots a cladogram- or phenogram-like rooted tree diagram
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-intreefile]        tree       Phylip tree file
      [-plotfile]          outfile    [*.fdrawgram] Phylip drawgram output file

       Additional (Optional) qualifiers (* if not always prompted):
       -[no]grows          boolean    [Y] Tree grows horizontally
       -style              menu       [c] Tree style output (Values: c (cladogram
                                      (v-shaped)); p (phenogram (branches are
                                      square)); v (curvogram (branches are 1/4 out
                                      of an ellipse)); e (eurogram (branches
                                      angle outward, then up)); s (swooporam
                                      (branches curve outward then reverse)); o
                                      (circular tree))
       -plotter            menu       [l] Plotter or printer the tree will be
                                      drawn on (Values: l (Postscript printer file
                                      format); m (PICT format (for drawing
                                      programs)); j (HP 75 DPI Laserjet PCL file
                                      format); s (HP 150 DPI Laserjet PCL file
                                      format); y (HP 300 DPI Laserjet PCL file
                                      format); w (MS-Windows Bitmap); f (FIG 2.0
                                      drawing program format); a (Idraw drawing
                                      program format); z (VRML Virtual Reality
                                      Markup Language file); n (PCX 640x350 file
                                      format (for drawing programs)); p (PCX
                                      800x600 file format (for drawing programs));
                                      q (PCX 1024x768 file format (for drawing
                                      programs)); k (TeKtronix 4010 graphics
                                      terminal); x (X Bitmap format); v (POVRAY 3D
                                      rendering program file); r (Rayshade 3D
                                      rendering program file); h (Hewlett-Packard
                                      pen plotter (HPGL file format)); d (DEC
                                      ReGIS graphics (VT240 terminal)); e (Epson
                                      MX-80 dot-matrix printer); c
                                      (Prowriter/Imagewriter dot-matrix printer);
                                      t (Toshiba 24-pin dot-matrix printer); o
                                      (Okidata dot-matrix printer); b (Houston
                                      Instruments plotter); u (other (one you have
                                      inserted code for)))
       -previewer          menu       [x] Previewing device (Values: n (Will not
                                      be previewed); I i (MSDOS graphics screen
                                      m:Macintosh screens); x (X Windows display);
                                      w (MS Windows display); k (TeKtronix 4010
                                      graphics terminal); d (DEC ReGIS graphics
                                      (VT240 terminal)); o (Other (one you have
                                      inserted code for)))
       -lengths            boolean    [N] Use branch lengths from user trees
    *  -labelrotation      float      [90.0] Angle of labels (0 degrees is
                                      horizontal for a tree growing vertically)
                                      (Number from 0.000 to 360.000)
       -[no]rescaled       toggle     [Y] Automatically rescale branch lengths
    *  -bscale             float      [1.0] Centimeters per unit branch length
                                      (Any numeric value)
       -treedepth          float      [0.53] Depth of tree as fraction of its
                                      breadth (Number from 0.100 to 100.000)
       -stemlength         float      [0.05] Stem length as fraction of tree depth
                                      (Number from 0.010 to 100.000)
       -nodespace          float      [0.3333] Character height as fraction of tip
                                      spacing (Number from 0.100 to 100.000)
       -nodeposition       menu       [c] Position of interior nodes (Values: i
                                      (Intermediate between their immediate
                                      descendants); w (Weighted average of tip
                                      positions); c (Centered among their ultimate
                                      descendants); n (Innermost of immediate
                                      descendants); v (So tree is v shaped))
    *  -xmargin            float      [1.65] Horizontal margin (cm) (Number 0.100
                                      or more)
    *  -ymargin            float      [2.16] Vertical margin (cm) (Number 0.100 or
                                      more)
    *  -xrayshade          float      [1.65] Horizontal margin (pixels) for
                                      Rayshade output (Number 0.100 or more)
    *  -yrayshade          float      [2.16] Vertical margin (pixels) for Rayshade
                                      output (Number 0.100 or more)
       -paperx             float      [20.63750] Paper width (Any numeric value)
       -papery             float      [26.98750] Paper height (Number 0.100 or
                                      more)
       -pagesheight        float      [1] Number of trees across height of page
                                      (Number 1.000 or more)
       -pageswidth         float      [1] Number of trees across width of page
                                      (Number 1.000 or more)
       -hpmargin           float      [0.41275] Horizontal overlap (cm) (Number
                                      0.001 or more)
       -vpmargin           float      [0.53975] Vertical overlap (cm) (Number
                                      0.001 or more)

       Advanced (Unprompted) qualifiers:
       -fontfile           string     [font1] Fontfile name (Any string)

       Associated qualifiers:

       "-plotfile" associated qualifiers
       -odirectory2        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-intreefile] (Parameter 1) | tree | Phylip tree file | Phylogenetic tree |
[-plotfile] (Parameter 2) | outfile | Phylip drawgram output file | Output file | <*>.fdrawgram
Additional (Optional) qualifiers
-[no]grows | boolean | Tree grows horizontally | Boolean value Yes/No | Yes
-style | list | Tree style output |
c | (cladogram (v-shaped))
p | (phenogram (branches are square))
v | (curvogram (branches are 1/4 out of an ellipse))
e | (eurogram (branches angle outward, then up))
s | (swooporam (branches curve outward then reverse))
o | (circular tree)
| c
-plotter | list | Plotter or printer the tree will be drawn on |
l | (Postscript printer file format)
m | (PICT format (for drawing programs))
j | (HP 75 DPI Laserjet PCL file format)
s | (HP 150 DPI Laserjet PCL file format)
y | (HP 300 DPI Laserjet PCL file format)
w | (MS-Windows Bitmap)
f | (FIG 2.0 drawing program format)
a | (Idraw drawing program format)
z | (VRML Virtual Reality Markup Language file)
n | (PCX 640x350 file format (for drawing programs))
p | (PCX 800x600 file format (for drawing programs))
q | (PCX 1024x768 file format (for drawing programs))
k | (TeKtronix 4010 graphics terminal)
x | (X Bitmap format)
v | (POVRAY 3D rendering program file)
r | (Rayshade 3D rendering program file)
h | (Hewlett-Packard pen plotter (HPGL file format))
d | (DEC ReGIS graphics (VT240 terminal))
e | (Epson MX-80 dot-matrix printer)
c | (Prowriter/Imagewriter dot-matrix printer)
t | (Toshiba 24-pin dot-matrix printer)
o | (Okidata dot-matrix printer)
b | (Houston Instruments plotter)
u | (other (one you have inserted code for))
| l
-previewer | list | Previewing device |
n | (Will not be previewed)
I i | (MSDOS graphics screen m:Macintosh screens)
x | (X Windows display)
w | (MS Windows display)
k | (TeKtronix 4010 graphics terminal)
d | (DEC ReGIS graphics (VT240 terminal))
o | (Other (one you have inserted code for))
| x
-lengths | boolean | Use branch lengths from user trees | Boolean value Yes/No | No
-labelrotation | float | Angle of labels (0 degrees is horizontal for a tree growing vertically) | Number from 0.000 to 360.000 | 90.0
-[no]rescaled | toggle | Automatically rescale branch lengths | Toggle value Yes/No | Yes
-bscale | float | Centimeters per unit branch length | Any numeric value | 1.0
-treedepth | float | Depth of tree as fraction of its breadth | Number from 0.100 to 100.000 | 0.53
-stemlength | float | Stem length as fraction of tree depth | Number from 0.010 to 100.000 | 0.05
-nodespace | float | Character height as fraction of tip spacing | Number from 0.100 to 100.000 | 0.3333
-nodeposition | list | Position of interior nodes |
i | (Intermediate between their immediate descendants)
w | (Weighted average of tip positions)
c | (Centered among their ultimate descendants)
n | (Innermost of immediate descendants)
v | (So tree is v shaped)
| c
-xmargin | float | Horizontal margin (cm) | Number 0.100 or more | 1.65
-ymargin | float | Vertical margin (cm) | Number 0.100 or more | 2.16
-xrayshade | float | Horizontal margin (pixels) for Rayshade output | Number 0.100 or more | 1.65
-yrayshade | float | Vertical margin (pixels) for Rayshade output | Number 0.100 or more | 2.16
-paperx | float | Paper width | Any numeric value | 20.63750
-papery | float | Paper height | Number 0.100 or more | 26.98750
-pagesheight | float | Number of trees across height of page | Number 1.000 or more | 1
-pageswidth | float | Number of trees across width of page | Number 1.000 or more | 1
-hpmargin | float | Horizontal overlap (cm) | Number 0.001 or more | 0.41275
-vpmargin | float | Vertical overlap (cm) | Number 0.001 or more | 0.53975
Advanced (Unprompted) qualifiers
-fontfile | string | Fontfile name | Any string | font1
Associated qualifiers
"-plotfile" associated outfile qualifiers
-odirectory2 -odirectory_plotfile | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

fdrawgram reads ...

### Input files for usage example

### File: drawgram.tree

    (Delta,(Epsilon,(Gamma,(Beta,Alpha))));

## Output file format

fdrawgram output ...

### Output files for usage example

### Graphics File: drawgram.fdrawgram

## Data files

The font file has a default name of "fontfile". If there is no file of that name, the program will ask you for the name of a font file (we provide ones that have the names font1 through font6). Once you decide on a favorite one of these, you could make a copy of it and call it fontfile, and it will then be used by default.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
fdrawtree | Plots an unrooted tree diagram
fretree | Interactive tree rearrangement

## Author(s)

This program is an EMBOSS conversion of a program written by Joe Felsenstein as part of his PHYLIP package.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

Written (2004) - Joe Felsenstein, University of Washington.

Converted (August 2004) to an EMBASSY program by the EMBOSS team.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

    None