Difference between revisions of "BioGraphics:generic glyph"
From GMOD
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+ | [[Image:generic.png|right|frame|The "generic" glyph]] | ||
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'''NAME''' | '''NAME''' | ||
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'''SYNOPSIS''' | '''SYNOPSIS''' | ||
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'''OPTIONS DEFINED IN THIS GLYPH''' | '''OPTIONS DEFINED IN THIS GLYPH''' | ||
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'''INHERITED OPTIONS''' | '''INHERITED OPTIONS''' | ||
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'''COLOR OPTIONS''' | '''COLOR OPTIONS''' | ||
See [[Glyphs_and_Glyph_Options#Colors]] | See [[Glyphs_and_Glyph_Options#Colors]] |
Revision as of 16:02, 19 April 2012
NAME
The generic glyph.
SYNOPSIS
This glyph draws genomic features as rectangles. If the feature contains subfeatures, each subfeature is rendered as a separate rectangle. The subfeatures can be connected by lines of various sorts using the "connector" option. Features can be named with a label at the top, and annotated with a descriptive string at the bottom.
See the Bio::Graphics::Glyph::generic manual page for full details.
$panel->add_track($features, -glyph => generic, -option1 => $value1, -option2 => $value2...);
To experiment with this glyph's options, use the glyph_help.pl script with either the -v or -p switch. Run "glyph_help -help" for details.
OPTIONS DEFINED IN THIS GLYPH
Option | Option Type | Description | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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-arrowhead | <'regular', 'filled'> [default regular] | Set the style of arrowhead used when drawing a stranded feature. "regular" will generate a thin arrowhead that protrudes from the feature. "filled" will taper the feature itself to turn it into an arrowhead. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-basecolor | <color> [default black] | The color to use for drawing DNA/protein residues at the base level See next section for color choices. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-connector | <'hat', 'solid', 'quill', 'dashed', 'crossed', 'undef'> [default 'undef'] | Type of line to use for connecting discontinuous pieces of the feature. Leave this undef to draw no connector at all. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-connector_color | <color> [default black] | Color to use for lines connecting discontinuous pieces of the feature. See next section for color choices. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-description | <string> [default 'undef'] | Whether to place a description underneath the feature. A value of 1 will describe the feature using the values returned by its source_tag() method. Any other true value will label the feature with the provided value. Undef will suppress labeling entirely. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-descriptioncolor | <color> [default black] | The color to use for drawing description text in this glyph (also known as font2color. See next section for color choices. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-draw_dna | <boolean> [default 'undef' (false)] | If true, draw the dna residues when magnification level allows (assumes that the feature is attached to a DNA sequence. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-draw_translation | <boolean> [default 'undef' (false)] | Draw the protein translation of the feature (assumes that the feature is attached to a DNA sequence. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-font | [default gdSmall'Font] | Font for glyph label and description. Valid choices: 'gdTiny'Font', 'gdSmall'Font', 'gdMedium'Bold'Font', 'gdLarge'Font', 'gdGiant'Font' | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-font2color | <color> [default black] | The color to use for drawing description text in this glyph (also known as descriptioncolor. See next section for color choices. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-fontcolor | <color> [default black] | The color to use for drawing label text in this glyph (also known as labelcolor). See next section for color choices. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-label | <string> [default 'undef'] | Whether to label the feature. A value of 1 will label the feature with the value returned by its display_name() method. Any other true value will label the feature with the provided value. Undef will suppress labeling entirely. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-label_position | <'top', 'left', 'alignment_left'> [default top] | Where to place the feature label. "top" will place the label above the glyph aligned with its left side. "left" will place the label to the left of the glyph, vertically centered with it. "alignment_left" will place the label to the left of the glyph in the panel pad-left positon. The last option is used internally for drawing DNA alignments which span the screen. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-labelcolor | <color> [default black] | The color to use for drawing label text in this glyph (also known as fontcolor). See next section for color choices. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-pad_bottom | <integer> [default 0] | Additional whitespace (in pixels) to add to the bottom of this glyph. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-pad_left | <integer> [default 0] | Additional whitespace (in pixels) to add to the left of this glyph. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-pad_right | <integer> [default 0] | Additional whitespace (in pixels) to add to the right of this glyph. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-pad_top | <integer> [default 0] | Additional whitespace (in pixels) to add to the top of this glyph. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-part_labels | <boolean> [default 'undef' (false)] | If false, do not label subparts of the feature. If equal to a value of 1, subparts are labeled with their display_name(). Any other true value, will be used as the subpart label. A false value suppresses the printing of subpart labels. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-record_label_positions | <integer> [default 'undef'] | If true, remember the coordinates of the glyph label and return it by calling $panel->key_boxes. If -1, then remember coordinates, but don't actually draw the label
INHERITED OPTIONS
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