.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.if !\nF .nr F 0
.if \nF>0 \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    if !\nF==2 \{\
.        nr % 0
.        nr F 2
.    \}
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "Bio::Graphics::Glyph::wiggle_density 3pm"
.TH Bio::Graphics::Glyph::wiggle_density 3pm "2018-09-21" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Graphics::Glyph::wiggle_density \- A density plot compatible with dense "wig"data
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This glyph works like the regular density but takes value data in
Bio::Graphics::Wiggle file format:
.PP
.Vb 4
\& reference = chr1
\& ChipCHIP Feature1 1..10000 wigfile=./test.wig;wigstart=0
\& ChipCHIP Feature2 10001..20000 wigfile=./test.wig;wigstart=656
\& ChipCHIP Feature3 25001..35000 wigfile=./test.wig;wigstart=1312
.Ve
.PP
The \*(L"wigfile\*(R" attribute gives a relative or absolute pathname to a
Bio::Graphics::Wiggle format file. The optional \*(L"wigstart\*(R" option
gives the offset to the start of the data. If not specified, a linear
search will be used to find the data. The data consist of a packed
binary representation of the values in the feature, using a constant
step such as present in tiling array data.
.SS "\s-1OPTIONS\s0"
.IX Subsection "OPTIONS"
The same as the regular graded_segments glyph, except that the
following options are recognized:
.PP
.Vb 2
\&   Name        Value        Description
\&   \-\-\-\-        \-\-\-\-\-        \-\-\-\-\-\-\-\-\-\-\-
\&
\&   basedir     path         Path to be used to resolve "wigfile" and "densefile"
\&                                tags giving relative paths. Default is to use the
\&                                current working directory. Absolute wigfile &
\&                                densefile paths will not be changed.
\&
\&   autoscale   "local" or "global"
\&                             If one or more of min_score and max_score options 
\&                             are absent, then these values will be calculated 
\&                             automatically. The "autoscale" option controls how
\&                             the calculation is done. The "local" value will
\&                             scale values according to the minimum and maximum
\&                             values present in the window being graphed. "global"   
\&                             will use chromosome\-wide statistics for the entire
\&                             wiggle or dense file to find min and max values.
\&
\&   smoothing   method name  Smoothing method: one of "mean", "max", "min" or "none"
\&
\&   smoothing_window 
\&               integer      Number of values across which data should be smoothed.
\&
\&   bicolor_pivot
\&               name         Where to pivot the two colors when drawing bicolor plots.
\&                               Options are "mean" and "zero". A numeric value can
\&                               also be provided.
\&
\&   pos_color   color        When drawing bicolor plots, the fill color to use for values
\&                              that are above the pivot point.
\&
\&   neg_color   color        When drawing bicolor plots, the fill color to use for values
\&                              that are below the pivot point.
.Ve
.SS "\s-1SPECIAL FEATURE TAGS\s0"
.IX Subsection "SPECIAL FEATURE TAGS"
The glyph expects one or more of the following tags (attributes) in
feature it renders:
.PP
.Vb 2
\&   Name        Value        Description
\&   \-\-\-\-        \-\-\-\-\-        \-\-\-\-\-\-\-\-\-\-\-
\&
\&   wigfile     path name    Path to the Bio::Graphics::Wiggle file for vales.
\&                            (required)
\&
\&   densefile   path name    Path to a Bio::Graphics::DenseFeature object
\&                               (deprecated)
\&
\&   denseoffset integer      Integer offset to where the data begins in the
\&                               Bio::Graphics::DenseFeature file (deprecated)
\&
\&   densesize   integer      Integer size of the data in the Bio::Graphics::DenseFeature
\&                               file (deprecated)
.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::arrow,
Bio::Graphics::Glyph::cds,
Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond,
Bio::Graphics::Glyph::dna,
Bio::Graphics::Glyph::dot,
Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow,
Bio::Graphics::Glyph::generic,
Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments,
Bio::Graphics::Glyph::line,
Bio::Graphics::Glyph::pinsertion,
Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect,
Bio::Graphics::Glyph::segments,
Bio::Graphics::Glyph::ruler_arrow,
Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript,
Bio::Graphics::Glyph::transcript2,
Bio::Graphics::Glyph::translation,
Bio::Graphics::Glyph::allele_tower,
Bio::DB::GFF,
Bio::SeqI,
Bio::SeqFeatureI,
Bio::Das,
\&\s-1GD\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <steinl@cshl.edu>.
.PP
Copyright (c) 2007 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.