changeset 9:dd2fdd397831 draft

Uploaded

--- a/circos-files/synteny-region-default.conf~	Tue May 06 05:09:31 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,115 +0,0 @@
-# The <ideogram> block defines the position, size, labels and other
-# properties of the segments on which data are drawn. These segments
-# are usually chromosomes, but can be any integer axis.
-
-<colors>
-<<include etc/colors.synteny.conf>>
-<<include etc/colors.mouse.conf>>
-</colors>
-
-<ideogram>
-
-<spacing>
-# Spacing between ideograms. Suffix "r" denotes a relative value. It
-# is relative to circle circumference (e.g. space is 0.5% of
-# circumference).
-default = 0.005r
-</spacing>
-
-# Ideogram position, thickness and fill. 
-#
-# Radial position within the image of the ideograms. This value is
-# usually relative ("r" suffix).
-radius           = 0.65r
-
-# Thickness of ideograms, which can be absolute (e.g. pixels, "p"
-# suffix) or relative ("r" suffix). When relative, it is a fraction of
-# image radius.
-thickness        = 30p
-
-# Ideograms can be drawn as filled, outlined, or both. When filled,
-# the color will be taken from the last field in the karyotype file,
-# or set by chromosomes_colors. Color names are discussed in
-#
-# http://www.circos.ca/documentation/tutorials/configuration/configuration_files
-#
-# When stroke_thickness=0p or if the parameter is missing, the ideogram is
-# has no outline and the value of stroke_color is not used.
-
-fill             = yes   # A
-
-stroke_color     = dgrey # B
-stroke_thickness = 1p    # B
-
-# Minimum definition for ideogram labels.
-
-show_label       = yes
-# see etc/fonts.conf for list of font names
-label_font       = bold
-label_radius     = (dims(ideogram,radius_inner)+dims(ideogram,radius_outer)-conf(ideogram,label_size))/2
-label_with_tag   = yes
-
-label_size       = 14 
-label_color = white
-label_parallel   = yes
-
-
-</ideogram>
-
-
-
-show_ticks          = yes
-show_tick_labels    = yes
-
-<ticks>
-
-radius           = 1r
-color            = black
-thickness        = 1p
-
-# the tick label is derived by multiplying the tick position
-# by 'multiplier' and casting it in 'format':
-#
-# sprintf(format,position*multiplier)
-
-multiplier       = 1e-6
-
-# %d   - integer
-# %f   - float
-# %.1f - float with one decimal
-# %.2f - float with two decimals
-#
-# for other formats, see http://perldoc.perl.org/functions/sprintf.html
-
-format           = %d
-
-<tick>
-spacing        = 0.1u
-size           = 5p
-</tick>
-
-<tick>
-spacing        = 1u
-size           = 10p
-show_label     = yes
-label_size     = 12p
-label_offset   = 10p
-format         = %d
-</tick>
-
-</ticks>
-
-#
-# These should be present in every Circos configuration file and
-# overridden as required. To see the content of these files, 
-# look in etc/ in the Circos distribution.
-
-
-
-# RGB/HSV color definitions, color lists, location of fonts, fill patterns.
-# Included from Circos distribution.
-<<include etc/colors_fonts_patterns.conf>> 
-
-# Debugging, I/O an dother system parameters
-# Included from Circos distribution.
-<<include etc/housekeeping.conf>> 

Binary file syntenyMapper.jar has changed