Bio::Graphics::Glyph::heat_map.3pm

Langue: en

Autres versions - même langue

Version: 2009-06-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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.