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.IX Title "Bio::Graphics::Glyph::heat_map 3pm"
.TH Bio::Graphics::Glyph::heat_map 3pm "2016-12-20" "perl v5.24.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Graphics::Glyph::heat_map \- The "heat_map" glyph
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
See Bio::Graphics::Panel and Bio::Graphics::Glyph.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This glyph draws \*(L"scored\*(R" features using a continuous
color gradient is the \s-1HSV\s0 color space. The color of 
each segment is proportionate to the score.
.SH "OPTIONS"
.IX Header "OPTIONS"
.SS "Global glyph options:"
.IX Subsection "Global glyph options:"
See Bio::Graphics::Glyph::generic
.SS "Glyph-specific options:"
.IX Subsection "Glyph-specific options:"
The color_map glyph recognizes the following
glyph-specific options:
.PP
.Vb 2
\&  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\*(Aqs "score" attribute
\&
\&  \-min_score   Minimum value of the         Calculated
\&               feature\*(Aqs "score" attribute
\&
\&  \-vary_fg     Vary the foreground color    1 (true)
\&               with the background color
.Ve
.PP
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.
.SS "Color Gradients"
.IX Subsection "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, \*(L"pure\*(R" 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).
.PP
Using the \*(L"pure_hue\*(R" 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.
.PP
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.
.PP
For the start_color and end_color options, 140 named webcolors
and their corresponsing \s-1RGB\s0 hex codes (listed below) are supported.
.PP
.Vb 10
\& 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
.Ve
.SH "BUGS"
.IX Header "BUGS"
Please report them.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Graphics::Panel,
Bio::Graphics::Glyph,
Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments,
Bio::Graphics::Feature,
Bio::DB::GFF
\&\s-1GD\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Sheldon McKay <mckays@cshl.edu>
.PP
Copyright (c) 2006 Cold Spring Harbor Laboratory
.PP
This package and its accompanying libraries is free software; you can
redistribute it and/or modify it under the terms of the \s-1GPL \s0(either
version 1, or at your option, any later version) or the Artistic
License 2.0.  Refer to \s-1LICENSE\s0 for the full license text. In addition,
please see \s-1DISCLAIMER\s0.txt for disclaimers of warranty.