Bio::Graphics::Glyph::heat_map - The "heat_map" glyph

- NAME
- SYNOPSIS
- DESCRIPTION
- OPTIONS

- Global glyph options:
- Glyph-specific options:
- Color Gradients

- BUGS
- SEE ALSO
- AUTHOR

# NAME

Bio::Graphics::Glyph::heat_map - The "heat_map" glyph

# SYNOPSIS

See the Bio::Graphics::Panel manpage and the Bio::Graphics::Glyph manpage.

# DESCRIPTION

This glyph draws "scored" features using a continuous color gradient is the HSV color space. The color of each segment is proportionate to the score.

# OPTIONS

## Global glyph options:

See the Bio::Graphics::Glyph::generic manpage

## Glyph-specific options:

The color_map glyph recognizes the following glyph-specific options:

      Option      Description                   Default
      ------      -----------                   -------

      -start_color Beginning of the color       white
                   gradient, expressed as a
                   named color or RGB hex
                   string

      -end_color   End of the color gradient    red

      -brightness  Color brilliance:  0-100     Calculated
                   This will override the
                   value from the named
                   color

      -saturation  Color saturation: 0-100      Calculated
                   This will override the
                   value from the named
                   color

      -pure_hue    Use the pure hue (bright-    0 (false)
                   ness and saturation both
                   at 100) for the named coloe

      -max_score   Maximum value of the         Calculated
                   feature's "score" attribute

      -min_score   Minimum value of the         Calculated
                   feature's "score" attribute

      -vary_fg     Vary the foreground color    1 (true)
                   with the background color

If max_score and min_score are not specified, the glyph will calculate the local maximum and minimum scores at run time. If single features, unaggregated features, or multiple aggregates are being drawn, this will result in an inconsistent color scale. It is recommended that global maximum and minimum scores be specified in the track configuration. Since many scoring functions are exponential, you may wish to take the log of your scores before passing them to this glyph.

## Color Gradients

The color gradient is calculating by progressing along the rainbow spectrum from red to violet, also incrementing brightness and saturation, all proportate to the score value. To vary the hue only, "pure" hues can be used. Pure hues have brightness and saturation values of 100. Some examples, in order, are red, yellow, lime, aqua/cyan, blue and magenta. The gradient can progress in reverse orientation with the respect to the visible light spectrum if a lower-order color is used as the start and a higher order color used as the end (for example lime->red).

Using the "pure_hue" option results in a brighter, more vibrant color spectrum, Choosing darker start and end colors, such as green or maroon, will result in a darker spectrum. A single color spectrum can be created by using black or white as the start or end color.

A grayscale spectrum will result if black and white are used as start and end colors. One example of an effective visual heat map is to progress from white->red.

For the start_color and end_color options, 140 named webcolors and their corresponsing RGB hex codes (listed below) are supported.

     steelblue              #4682B4
     royalblue              #041690
     cornflowerblue         #6495ED
     lightsteelblue         #B0C4DE
     mediumslateblue        #7B68EE
     slateblue              #6A5ACD
     darkslateblue          #483D8B
     midnightblue           #191970
     navy                   #000080
     darkblue               #00008B
     mediumblue             #0000CD
     blue                   #0000FF
     dodgerblue             #1E90FF
     deepskyblue            #00BFFF
     lightskyblue           #87CEFA
     skyblue                #87CEEB
     lightblue              #ADD8E6
     powderblue             #B0E0E6
     azure                  #F0FFFF
     lightcyan              #E0FFFF
     paleturquoise          #AFEEEE
     mediumturquoise        #48D1CC
     lightseagreen          #20B2AA
     darkcyan               #008B8B
     teal                   #008080
     cadetblue              #5F9EA0
     darkturquoise          #00CED1
     aqua                   #00FFFF
     cyan                   #00FFFF
     turquoise              #40E0D0
     aquamarine             #7FFFD4
     mediumaquamarine       #66CDAA
     darkseagreen           #8FBC8F
     mediumseagreen         #3CB371
     seagreen               #2E8B57
     darkgreen              #006400
     green                  #008000
     forestgreen            #228B22
     limegreen              #32CD32
     lime                   #00FF00
     chartreuse             #7FFF00
     lawngreen              #7CFC00
     greenyellow            #ADFF2F
     yellowgreen            #9ACD32
     palegreen              #98FB98
     lightgreen             #90EE90
     springgreen            #00FF7F
     mediumspringgreen      #00FA9A
     darkolivegreen         #556B2F
     olivedrab              #6B8E23
     olive                  #808000
     darkkhaki              #BDB76B
     darkgoldenrod          #B8860B
     goldenrod              #DAA520
     gold                   #FFD700
     yellow                 #FFFF00
     khaki                  #F0E68C
     palegoldenrod          #EEE8AA
     blanchedalmond         #FFEBCD
     moccasin               #FFE4B5
     wheat                  #F5DEB3
     navajowhite            #FFDEAD
     burlywood              #DEB887
     tan                    #D2B48C
     rosybrown              #BC8F8F
     sienna                 #A0522D
     saddlebrown            #8B4513
     chocolate              #D2691E
     peru                   #CD853F
     sandybrown             #F4A460
     darkred                #8B0000
     maroon                 #800000
     brown                  #A52A2A
     firebrick              #B22222
     indianred              #CD5C5C
     lightcoral             #F08080
     salmon                 #FA8072
     darksalmon             #E9967A
     lightsalmon            #FFA07A
     coral                  #FF7F50
     tomato                 #FF6347
     darkorange             #FF8C00
     orange                 #FFA500
     orangered              #FF4500
     crimson                #DC143C
     red                    #FF0000
     deeppink               #FF1493
     fuchsia                #FF00FF
     magenta                #FF00FF
     hotpink                #FF69B4
     lightpink              #FFB6C1
     pink                   #FFC0CB
     palevioletred          #DB7093
     mediumvioletred        #C71585
     purple                 #800080
     darkmagenta            #8B008B
     mediumpurple           #9370DB
     blueviolet             #8A2BE2
     indigo                 #4B0082
     darkviolet             #9400D3
     darkorchid             #9932CC
     mediumorchid           #BA55D3
     orchid                 #DA70D6
     violet                 #EE82EE
     plum                   #DDA0DD
     thistle                #D8BFD8
     lavender               #E6E6FA
     ghostwhite             #F8F8FF
     aliceblue              #F0F8FF
     mintcream              #F5FFFA
     honeydew               #F0FFF0
     lightgoldenrodyellow   #FAFAD2
     lemonchiffon           #FFFACD
     cornsilk               #FFF8DC
     lightyellow            #FFFFE0
     ivory                  #FFFFF0
     floralwhite            #FFFAF0
     linen                  #FAF0E6
     oldlace                #FDF5E6
     antiquewhite           #FAEBD7
     bisque                 #FFE4C4
     peachpuff              #FFDAB9
     papayawhip             #FFEFD5
     beige                  #F5F5DC
     seashell               #FFF5EE
     lavenderblush          #FFF0F5
     mistyrose              #FFE4E1
     snow                   #FFFAFA
     white                  #FFFFFF
     whitesmoke             #F5F5F5
     gainsboro              #DCDCDC
     lightgrey              #D3D3D3
     silver                 #C0C0C0
     darkgray               #A9A9A9
     gray                   #808080
     lightslategray         #778899
     slategray              #708090
     dimgray                #696969
     darkslategray          #2F4F4F
     black                  #000000

# BUGS

Please report them.

# SEE ALSO

the Bio::Graphics::Panel manpage, the Bio::Graphics::Glyph manpage, the Bio::Graphics::Glyph::graded_segments manpage, the Bio::Graphics::Glyph::heterogeneous_segments manpage, the Bio::Graphics::Feature manpage, the Bio::DB::GFF manpage GD

# AUTHOR

Sheldon McKay <mckays@cshl.edu>

Copyright (c) 2006 Cold Spring Harbor Laboratory

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.

Bio::Graphics::Glyph::heat_map - The "heat_map" glyph