genome visualization with Circos_ session 1 Lesson 1 Drawing and Spacing Ideograms

copyright :Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645

thanks to the handsome tools  and the creative teams, I have the chance to enjoy the journey of drawing amazing pictures.  The software, circos-0.69-6, will be my great work partner. The course materials , software files and something new reedited   for the purpoes of learning will be present here. To save time , list the citation only one time here.  Thanks for the authors' great work.

 

Lesson 1  Drawing and Spacing Ideograms

paraments and files annotation :

  karyotype:  size  and name of chromsome

   units        : unit of length for the chromosome

   display default :  yes /no ,  appearance order

   ideogram.conf : spacing, position, thickness,  color/outline format of the ideogram

   ticks.conf : position, label, spacing, and grids for tick marks

   image.conf :  size, location, format of the output image

   Colors_Fonts_Patterns.conf ： color, Fonts, and fill patterns

   housekeeping.conf : file delimiters, debugging options and other global settings

 

defining a karyotype:

   karyotype file : defines the name, size and colors of the chromosomes. any subset of the chromosomes  can be drawn.

  <colors>  block ： defined in the etc/colors_fonts_patterns.conf file .  colors are predefined for each hue.:

# etc/colors_fonts_patterns.conf
<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<patterns>
<<include etc/patterns.conf>>
</patterns>
~                                                                                                                                                             
~            

# etc/colors.conf
# HUE   (e.g. red)
# dHUE  (dark HUE, e.g. dred)
# vdHUE (very dark HUE, e.g. vdred))
# vvdHUE (very very dark HUE, e.g. vvdred))
#
# Pure colors are prefixed with "p" (e.g. pred, dpred, vdpred) and 
# are based on 10% luminance steps from a pure hue color. Use these
# at your discretion.
#
# Boutique colors are not. If you really must use 'bisque', then add
#
# bisque = 255,228,196
#
# See colors.unixnames.txt for a large number of named color definitions.
#
# In addition to hues, two other color groups are defined. 
#
# - cytogenetic band colors (e.g. gposNNN, acen, stalk, etc.) which
#   correspond to colors on ideogram bands
# - UCSC chromosome color palette (e.g. chrNN, chrUn, chrNA)
#     - included from ucsc.conf
# 
# Another useful list of colors is in brewer.conf, which defines
# Brewer Palettes (www.colorbrewer.org), and corresponding lists.
#
#

# 

white       = 255,255,255
vvvvlgrey   = greys-9-seq-1
vvvlgrey    = greys-9-seq-1
vvlgrey     = greys-9-seq-2
vlgrey      = greys-9-seq-3
lgrey       = greys-9-seq-4
grey        = greys-9-seq-5
dgrey       = greys-9-seq-6
vdgrey      = greys-9-seq-7
vvdgrey     = greys-9-seq-8
vvvdgrey    = greys-9-seq-9
vvvvdgrey   = greys-9-seq-9
black       = 0,0,0
                                                                                                                                            41,1          14%

# etc/colors_Brewer.conf
# Colors from www.ColorBrewer.org by Cynthia A. Brewer, 
# Geography, Pennsylvania State University. See BREWER for license. 
# See www.colorbrewer.org for details.
# 
# Color names are PALETTE-NUMCOLORS-TYPE-IDX (e.g. reds-3-seq-1)
#
#  PALETTE   palette name (e.g. reds)
#  NUMCOLORS number of colors in the palette (e.g. 3)
#  TYPE      palette type (div, seq, qual)
#  IDX       color index within the palette (e.g. 1)
#
# Another version of the color index is defined where COLORCODE is the
# color's letter unique to a given PALETTE.
#
# For each palette, two color list are defined for use with heatmaps.
#
#   PALETTE-NUMCOLORS-TYPE
#   PALETTE-NUMCOLORS-TYPE-rev
#
# where the second contains colors in reversed order.
#
# Also supported is the format
#
#   PALETTE-NUMCOLORS
#   PALETTE-NUMCOLORS-rev
#
# (without the -TYPE), which isn't necessary to uniquely identify the palette.
#
# Each diverging and sequential palette has all the colors used for 
# its n-color variants listed an integrated 13-color (for sequential)
# or 15-color (for diverging) palettes.
#
# http://www.personal.psu.edu/cab38/ColorBrewer/ColorBrewer_updates.html
# http://mkweb.bcgsc.ca/brewer
#
#

blues-3-seq = blues-3-seq-(\d+)
blues-3-seq-rev = rev(blues-3-seq-(\d+))
blues-3-seq-1 = 222,235,247
blues-3-seq-2 = 158,202,225
blues-3-seq-3 = 49,130,189
                                                                                                                                            1,1           Top

 

[arthur@localhost 1]$ circos
debuggroup summary 0.47s welcome to circos v0.69-6 31 July 2017 on Perl 5.016003
debuggroup summary 0.48s current working directory /home/arthur/BGA2017/Course_material/June08/circos-course/session/1/1
debuggroup summary 0.48s command /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/circos [no flags]
debuggroup summary 0.48s guessing configuration file
debuggroup summary 0.48s found conf file /home/arthur/BGA2017/Course_material/June08/circos-course/session/1/1/etc/circos.conf
debuggroup summary 1.05s debug will appear for these features: output,summary
debuggroup summary 1.05s bitmap output image ./circos.png
debuggroup summary 1.05s parsing karyotype and organizing ideograms
debuggroup summary 1.07s karyotype has 5 chromosomes of total size 185,000,005
debuggroup summary 1.07s applying global and local scaling
debuggroup summary 1.08s allocating image, colors and brushes
debuggroup summary 4.53s drawing 5 ideograms of total size 185,000,005
debuggroup summary 4.53s drawing highlights and ideograms
debuggroup output 4.76s generating output
debuggroup output 4.87s created PNG image ./circos.png (57 kb)
[arthur@localhost 1]$ ls
circos.png  circos.svg  etc  misc
[arthur@localhost 1]$ eog circos.png

figure2

 

spacing between ideograms

the u suffix indicates that the units of this value are given relative to the value defined by chromosome_units. Since chromosomes_units = 1000000, the spacing is 2000000(2Mb)

[arthur@localhost etc]$ ls
circos.conf  ideogram.conf
#ideogram spacing default 2u to 10u
[arthur@localhost etc]$ vim ideogram.conf 



[arthur@localhost 1]$ circos
debuggroup summary 0.41s welcome to circos v0.69-6 31 July 2017 on Perl 5.016003
debuggroup summary 0.41s current working directory /home/arthur/BGA2017/Course_material/June08/circos-course/session/1/1
debuggroup summary 0.41s command /home/arthur/BGA2017/Course_material/circos/circos-0.69-6/bin/circos [no flags]
debuggroup summary 0.41s guessing configuration file
debuggroup summary 0.41s found conf file /home/arthur/BGA2017/Course_material/June08/circos-course/session/1/1/etc/circos.conf
debuggroup summary 0.77s debug will appear for these features: output,summary
debuggroup summary 0.77s bitmap output image ./circos.png
debuggroup summary 0.77s parsing karyotype and organizing ideograms
debuggroup summary 0.79s karyotype has 5 chromosomes of total size 185,000,005
debuggroup summary 0.79s applying global and local scaling
debuggroup summary 0.80s allocating image, colors and brushes
debuggroup summary 4.48s drawing 5 ideograms of total size 185,000,005
debuggroup summary 4.48s drawing highlights and ideograms
debuggroup output 4.74s generating output
debuggroup output 4.82s created PNG image ./circos.png (59 kb)
[arthur@localhost 1]$ ls 
circos.png  circos.svg  etc  misc
[arthur@localhost 1]$ eog circos.png

figure 3

 

spacing between specific pairs of ideograms

#spacing on either side of ch1 will be changed

<pairwise ch1>

spacing = 5u

</pairwise> 

#Spacing between individual ideograms pairs can be ajusted

<pairwise ch2 ch3>

spacing = 15u

</pairwise>

<ideogram>

<spacing>

#default = 2u

default = 10u

<pairwise chr1>
spacing = 5u
</pairwise>

#<pairwise chr2 chr3>
#spacing = 15u
#</pairwise>

#<pairwise chr3 chr4>
#spacing = 25u
#</pairwise>

</spacing>

<<include ../../etc/ideogram.conf>>

</ideogram>

the space adjacent to ch1  is changed from 10u to 5u

figure 4

 

the spacing between chromosome 2 and chromosome 3 is increased from 10u to 15u and between chromosome 3 and chromosome 4 10u to 25u .

figure 5