Bio::Graphics::Glyph::vista_plot3pm

Usage

Overview

This glyph draws peak calls (features with discreet boundaries, i.e. putative transcription sites, over signal graph (wiggle_xyplot) requires a special load gff file that uses attributes 'wigfile' and 'peak_type'

Example:

2L chip_seq vista 5407 23011573 . . . Name=ChipSeq Exp 1;wigfile=SomeWigFile.wigdb;peak_type=binding_site:exp1

The glyph will draw the wiggle file first, than overlay the peaks (if there are any) over signal graph. Elsewhere in the GFF3 file, there should be one or more features of type "binding_site:exp1", e.g.:

2L exp1 binding_site 91934 92005 . . .

Options like 'balloon hover' and 'link' are available to customize interaction with peaks in detail view.

BigWig support:

Supported bigwig format also requires another attribute to be supplied in load gff file (fasta) which specifies sequence index file for the organism in use. The data file should have the 'bw' extension - it is used to detect the BigWig format by vista_plot

3L chip_seq vista 1 24543530 . . . Name=ChipSeq Exp 2;wigfile=SomeBigWigFile.bw;peak_type=binding_site:exp2;fasta=YourOrganism.fasta

Note that all attributes should be present in load gff, as the code currently does not handle situation when only some of the attributes are in gff. To omit peak or signal drawing use "" (i.e. peak_type="") In both cases, the stanza code will look the same (only essential parameters shown):

 [VISTA_PLOT]
 feature         = vista:chip_seq
 glyph           = vista_plot
 label           = 1 
 smoothing       = mean
 smoothing_window = 10
 bump density    = 250
 autoscale       = local
 variance_band   = 1
 max_peak        = 255
 min_peak        = 1
 peakwidth       = 3
 start_color     = lightgray
 end_color       = black
 pos_color       = blue
 neg_color       = orange
 bgcolor         = orange
 alpha           = 80
 fgcolor         = black
 database        = database_with_load_gff_data
 box_subparts    = 1
 bicolor_pivot   = min
 key             = VISTA plot

Options

Options are the same as for wiggle_xyplot and heat_map

Additional parameters:

alpha set transparency for peak area.

glyph_subtype Display only 'peaks', 'signal', 'density' or 'peaks+signal'. Aliases for 'peaks+signal' include "both" and "vista".

Recommended global settings:

for proper peak drawing transparency should be enabled by setting truecolors=1 in GBrowse.conf file