circos - Session 2 - Lesson 1 - Ideogram, Tick, Grid and Label Layout

review configuration file for this lesson

#shared by all lessons in this session
<<include ../etc/karyotype.and.layout.conf>>
<<include ../etc/ideogram.conf>>
<<include ../etc/ticks.conf>>

#shared by all sessions
<<include ../../etc/image.conf>>

#from Circos distribution
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>

../etc/karyotype.and.layout.conf is a file that is shared by all the lessons in this session. It will be included in each lesson's circos.conf

karyotype = data/karyotype/karyotype.human.txt,data/karyotype/karyotype.mouse.txt

chromosomes_units           = 1000000
chromosomes_display_default = no

chromosomes       = hs1;hs2;mm1;mm2
chromosomes_order = hs1,hs2,mm2,mm1
chromosomes_color = hs1=rdylbu-11-div-2,hs2=rdylbu-11-div-3,mm1=rdylbu-11-div-10,mm2=rdylbu-11-div-9

chromosomes_reverse = /mm/
chromosomes_scale   = /./=0.25r

<highlights>
<highlight>
file = ../data/highlight.txt
r0   = 1r+40p
r1   = 1r+45p
</highlight>
</highlights>

Introduction to brewer palettes

http://mkweb.bcgsc.ca/brewer/swatches/brewer-palettes-swatches.pdf