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 whitegradient, expressed as anamed color or RGB hexstring-end_color End of the color gradient red-brightness Color brilliance: 0-100 CalculatedThis will override thevalue from the namedcolor-saturation Color saturation: 0-100 CalculatedThis will override thevalue from the namedcolor-pure_hue Use the pure hue (bright- 0 (false)ness and saturation bothat 100) for the named color-max_score Maximum value of the Calculatedfeature's "score" attribute-min_score Minimum value of the Calculatedfeature'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 corresponding RGB hex codes (listed below) are supported.
steelblue #4682B4royalblue #041690cornflowerblue #6495EDlightsteelblue #B0C4DEmediumslateblue #7B68EEslateblue #6A5ACDdarkslateblue #483D8Bmidnightblue #191970navy #000080darkblue #00008Bmediumblue #0000CDblue #0000FFdodgerblue #1E90FFdeepskyblue #00BFFFlightskyblue #87CEFAskyblue #87CEEBlightblue #ADD8E6powderblue #B0E0E6azure #F0FFFFlightcyan #E0FFFFpaleturquoise #AFEEEEmediumturquoise #48D1CClightseagreen #20B2AAdarkcyan #008B8Bteal #008080cadetblue #5F9EA0darkturquoise #00CED1aqua #00FFFFcyan #00FFFFturquoise #40E0D0aquamarine #7FFFD4mediumaquamarine #66CDAAdarkseagreen #8FBC8Fmediumseagreen #3CB371seagreen #2E8B57darkgreen #006400green #008000forestgreen #228B22limegreen #32CD32lime #00FF00chartreuse #7FFF00lawngreen #7CFC00greenyellow #ADFF2Fyellowgreen #9ACD32palegreen #98FB98lightgreen #90EE90springgreen #00FF7Fmediumspringgreen #00FA9Adarkolivegreen #556B2Folivedrab #6B8E23olive #808000darkkhaki #BDB76Bdarkgoldenrod #B8860Bgoldenrod #DAA520gold #FFD700yellow #FFFF00khaki #F0E68Cpalegoldenrod #EEE8AAblanchedalmond #FFEBCDmoccasin #FFE4B5wheat #F5DEB3navajowhite #FFDEADburlywood #DEB887tan #D2B48Crosybrown #BC8F8Fsienna #A0522Dsaddlebrown #8B4513chocolate #D2691Eperu #CD853Fsandybrown #F4A460darkred #8B0000maroon #800000brown #A52A2Afirebrick #B22222indianred #CD5C5Clightcoral #F08080salmon #FA8072darksalmon #E9967Alightsalmon #FFA07Acoral #FF7F50tomato #FF6347darkorange #FF8C00orange #FFA500orangered #FF4500crimson #DC143Cred #FF0000deeppink #FF1493fuchsia #FF00FFmagenta #FF00FFhotpink #FF69B4lightpink #FFB6C1pink #FFC0CBpalevioletred #DB7093mediumvioletred #C71585purple #800080darkmagenta #8B008Bmediumpurple #9370DBblueviolet #8A2BE2indigo #4B0082darkviolet #9400D3darkorchid #9932CCmediumorchid #BA55D3orchid #DA70D6violet #EE82EEplum #DDA0DDthistle #D8BFD8lavender #E6E6FAghostwhite #F8F8FFaliceblue #F0F8FFmintcream #F5FFFAhoneydew #F0FFF0lightgoldenrodyellow #FAFAD2lemonchiffon #FFFACDcornsilk #FFF8DClightyellow #FFFFE0ivory #FFFFF0floralwhite #FFFAF0linen #FAF0E6oldlace #FDF5E6antiquewhite #FAEBD7bisque #FFE4C4peachpuff #FFDAB9papayawhip #FFEFD5beige #F5F5DCseashell #FFF5EElavenderblush #FFF0F5mistyrose #FFE4E1snow #FFFAFAwhite #FFFFFFwhitesmoke #F5F5F5gainsboro #DCDCDClightgrey #D3D3D3silver #C0C0C0darkgray #A9A9A9gray #808080lightslategray #778899slategray #708090dimgray #696969darkslategray #2F4F4Fblack #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 <[email protected]>
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.