See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTIONThis glyph draws protein sequences. At high magnifications, this glyph will draw the actual amino acids of the sequence. At low magnifications, the glyph will plot the Kyte-Doolite hydropathy. By default, the KD plot will use a window size of 9 residues, but this can be changed by specifying the kd_window option.
The feature may return either a protein sequence or a DNA sequence in response to the seq() method. However, if it returns a DNA sequence, then the feature must also return the correct phase and strand in order for the glyph to translate its open reading frame correctly!
OPTIONSThe following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.
Option Description Default ------ ----------- ------- -fgcolor Foreground color black -outlinecolor Synonym for -fgcolor -bgcolor Background color turquoise -fillcolor Synonym for -bgcolor -linewidth Line width 1 -height Height of glyph 10 -font Glyph font gdSmallFont -connector Connector type 0 (false) -connector_color Connector color black -label Whether to draw a label 0 (false) -description Whether to draw a description 0 (false) -hilite Highlight color undef (no color)
In addition to the common options, the following glyph-specific options are recognized:
Option Description Default ------ ----------- ------- -do_kd Whether to draw the Kyte- true Doolittle hydropathy plot at low mags -kd_window Size of the sliding window 9 to use in the KD hydropathy calculation. -axis_color Color of the vertical axes fgcolor in the KD hydropathy plot -phase_style The way phase is to be interpreted. One of "012" "012" or "021"