Provided by: libbio-graphics-perl_2.40-2_all bug

NAME

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

SYNOPSIS

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

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 Bio::Graphics::Glyph::generic

   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 color

         -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

       Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::graded_segments,
       Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Feature, Bio::DB::GFF 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.