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NOTICE

Figures in the publication used actual data from the 
multi-patient follicular lymphoma study (see Methods). These
novel data are yet unpublished and therefore the data files 
included in this archive have been perturbed to secure the
original data until its publication. Figures for which data
has been perturbed are Figures 1, 5, 6, and 7.

The figures generated from the perturbed data are identical in
layout and format. Individual data points, however, are different
from published figures.
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To create the images 

1. download and install Circos 

   e.g.
   > cd /usr/local
   > wget http://mkweb.bcgsc.ca/circos/distribution/circos-0.49.tgz
   > tar xvfz circos-0.49.tgz
   > cd circos-0.49
   > cat README # read the requirements section and install required CPAN modules you do not have
   > ./install (for UNIX only)

2. set environment variable CIRCOS_PATH to the Circos installation directory

   e.g. 
   > export CIRCOS_PATH=/usr/local/circos-0.49

   The circos binary will be expected to be at

   $CIRCOS_PATH/bin/circos

3. for each figure, run the makefigure script

   > cd fig1
   > ./makefigure

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NOTE FOR FIGURES 1-7

Each figure will be created in both PNG and SVG formats. The PNG file will be 3000 x 3000 in size.
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NOTE FOR FIGURE 8

Figure 8 is a panel of 39 individual images. Each panel is annotated
with the chromosome number using Image Magick
(www.imagemagick.org). The 'convert' utility that comes with Image
Magick must be in your path.

Individual images in the panel will be created in fig8/images, in PNG
(3000x3000 pixels) and SVG formats. The panel will be created in
fig8/figure.png in PNG format (6000x7000 pixels).
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