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Overview

Circos is a software package for visualizing data and information in a circular layout, enabling the user to explore the relationships between objects or positions.ine control each element in the figure to tailor its focus points and detail to your audience.  Circos has been found by many to be suitable for publication-quality graphics.  This page contains some important tips on how to use Circos properly on the HPCC.

Configuration Files

The core of a Circos run revoles around the input data files and a Circos configuration file.  An example Circos configuration file is provided as reference below:

 

<<include ideogram.conf>>
<<include ticks.conf>>
 
<image>
<<include /opt/software/CIROCS/0.55--GCC-4.4.5/etc/image.conf>>
</image>
 
<colors>
<<include /opt/software/CIROCS/0.55--GCC-4.4.5/etc/colors.conf>>
<<include /opt/software/CIROCS/0.55--GCC-4.4.5/etc/brewer.conf>>
</colors>
 
<fonts>
<<include /opt/software/CIROCS/0.55--GCC-4.4.5/etc/fonts.conf>>
</fonts>
 
<<include /opt/software/CIROCS/0.55--GCC-4.4.5/etc/housekeeping.conf>>
show_links      = yes
show_heatmaps   = yes
show_highlights = yes
show_scatter    = yes
show_histogram  = yes
show_text       = yes
<<include karyotype.and.layout.conf>>
### links
<links>
show          = __$CONF{show_links}__
ribbon        = yes
flat          = yes
radius        = 0.45r-55p
bezier_radius = 0r
color         = black_a5
<link ratbundle>
file = exampledata/rn.bundle.txt
<<include link.rules.conf>>
</link>
 
### plots
<plots>
<<include highlights.conf>>
# some large human genes (list contains genes > 250kb in size)
<plot>
show   = __$CONF{show_text}__
type   = text
file   = exampledata/genes.txt
color  = black
r0     = 0.415r
r1     = 0.73r
label_size = 12p
label_font = default
 
rpadding = 0r
padding  = 0.1r
 
label_snuggle        = yes
max_snuggle_distance = 1r
snuggle_sampling     = 1
snuggle_tolerance    = 0.25r
 
show_links     = yes
link_dims      = 4p,2p,5p,2p,2p
link_thickness = 2p
link_color     = grey
 
<rules>
<rule>
importance = 100
condition  = _LABEL_ =~ /omim/
color      = blue # green
flow       = continue
</rule>
<rule>
importance = 100
condition  = _LABEL_ =~ /cancer/
color      = red
label_font = bold
flow       = continue
</rule>
<rule>
importance = 90
condition  = 1
value      = eval( my $x=_LABEL_; $x=~ s/_.+//; $x )
</rule>
</rules>
</plot>
# human->mouse and human->rat chain heatmaps
<plot>
show   = __$CONF{show_heatmaps}__
type   = heatmap
file   = exampledata/heatmap.hs.mm.20e6.txt
color  = blues-9-seq
min    = 0
max    = .20e6
r0     = 0.765r
r1     = 0.785r
stroke_color     = white
stroke_thickness = 1p
</plot>

 

If you're using local customizations of various sub-configuration files, make sure you use the correct path to those files.  

Alternately, when using the generic CIRCOS-supplied configuration files, make sure you use the correct path to the centralized CIRCOS install directory. For example:

 

<<include /opt/software/CIROCS/0.55--GCC-4.4.5/etc/image.conf>>

 

If you use the path provided in one of the default or sample CIRCOS configuration files, for example:

 

<<include ../etc/image.conf>>

 

This will throw an error, since the correct path will not be found.

Samples of the generic CIRCOS configuration files are supplied for your use in:

 

/mnt/research/common-data/Bio/CIRCOS

 

Notes on Caching

Caching files, such as those used for Colors calculation, will be stored by default in your run directory.  Originally, CIRCOS was hard-coded to use the /tmp directory.  However, due to access limitations on the HPCC, this has been changed to "./".