Author image Lincoln D. Stein
and 1 contributors

Documentation

Render a SearchIO parser report into a simple overview graphic
Render a Bio::Graphics Feature File
Render a Bio::Graphics Feature File on the web
Render a SearchIO parser report into a simple overview graphic

Modules

Generate GD images of Bio::Seq objects
A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag-gtvalue semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse).
draw a cartoon of an Alpha-helical transmembrane protein.
A simple feature object for use with Bio::Graphics::Panel
Compatibility module
A directory of feature files and conf files
A set of Bio::Graphics features, stored in a file
Iterator across a Bio::Graphics::FeatureFile
Base class for Bio::Graphics::Glyph objects
Factory for Bio::Graphics::Glyph objects
The "alignment" glyph
The "allele_tower" glyph
The "anchored_arrow" glyph
the "arrow" glyph
The "box" glyph
The "broken line" glyph
The "cds" glyph
The "christmas arrow" glyph
The "crossbox" glyph
The "dashed line" glyph
The "diamond" glyph
The "dna" glyph
The "dot" glyph
A glyph that draws a "dumbbell" with the same shapes on both ends.
The "ellipse" glyph
the "ex", or "crossed box" glyph
The "extending arrow" glyph
A base class fixed width glyphs
the "flag" glyph
A GFF3-compatible gene glyph
The "generic" glyph
The "graded_segments" glyph
The "group" glyph
The "hat" glyph
The "heat_map" glyph
The "heat_map_ideogram" glyph
The "heterogeneous_segments" glyph
The "hidden" glyph
An xyplot plot drawing dual graph using data from two or more wiggle files per track
The "ideogram" glyph
A glyph that draws photographs & other images
The "lightning" glyph
The "line" glyph
a base class which suppors semantic zooming of scored alignment features
The "merged_alignment" glyph
The minmax glyph
The "polycistronic operon" glyph
The "oval" glyph
The "pairwise plot" glyph
The "pentagram" glyph
The "phylogenetic alignment" glyph
The "Drosophila P-element Insertion" glyph
The "STS primers" glyph
The sequence ontology transcript glyph
The "protein" glyph
The "ragged ends" glyph
A GFF3-compatible gene glyph
The "redgreen_box" glyph
The "redgreen_segments" glyph
A glyph that draws the same shape repeatedly.
The "round rect" glyph
glyph for drawing an arrow as ruler (5' and 3' are marked as label)
The "saw teeth" glyph
The "scale" glyph
The "segmented_keyglyph" glyph
The "segments" glyph
The sequence ontology transcript glyph
The "span" glyph
The "spectrogram" glyph
The "splice_site" glyph
The stackedplot glyph
Draw ternary plot data
The "text in box" glyph
DAS-compatible package to use for drawing a line of groups of three letters
The "tic-tac-toe" glyph
The "too many to show" glyph
A glyph that visualizes a trace file
The "track" glyph
The "transcript" glyph
The "transcript2" glyph
The "6-frame translation" glyph
The "triangle" glyph
The "two bolts" glyph
The "vista_plot" glyph
The "wave" glyph
The "weighted arrow" glyph
The whiskerplot glyph
A generic box glyph compatible with dense "wig"data
A density plot compatible with dense "wig"data
An xyplot plot compatible with dense "wig"data
The xyplot glyph
Generate GD images of Bio::Seq objects
generate SVG output of Pictogram display for consensus motifs
A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.
non-object-oriented utilities used in Bio::Graphics modules
Binary storage for dense genomic features

Provides

in lib/Bio/Graphics/FeatureDir.pm
in lib/Bio/Graphics/Glyph/cross.pm
in lib/Bio/Graphics/Glyph/fb_shmiggle.pm
in lib/Bio/Graphics/Glyph/point_glyph.pm
in lib/Bio/Graphics/Glyph/read_pair.pm
in lib/Bio/Graphics/Glyph/smoothing.pm
in lib/Bio/Graphics/Glyph/wiggle_data.pm
in lib/Bio/Graphics/Glyph/wiggle_whiskers.pm
in lib/Bio/Graphics/Layout.pm
in lib/Bio/Graphics/Layout.pm
in lib/Bio/Graphics/Layout.pm
in lib/Bio/Graphics/Wiggle/Loader.pm