Bio::Graphics::Glyph::heat_map man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

Bio::Graphics::Glyph::User_Contributed Perl DBio::Graphics::Glyph::heat_map(3)

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.

perl v5.14.1			  2011-07-22 Bio::Graphics::Glyph::heat_map(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net