ideogram layout and formatting - mkweb.bcgsc.camkweb.bcgsc.ca/dev/circos/documentation/course/slides/session-2.pdf · GENOME VISUALIZATION WITH CIRCOS · Session 2 · Ideogram Layout

GENOME VISUALIZATION WITH CIRCOS v20120504

Stazione Zoologica Anton Dohrn, Naples - ItalyMay 7–19, 2012

EMBO PRACTICAL COURSE: BIOINFORMATICS AND COMPARATIVE GENOME ANALYSES

ideogram layout and formatting

Genome Sciences CenterBC Cancer AgencyVancouver, Canada

SESSION 2

MARTIN KRZYWINSKI

drawing and spacing ideograms

relative ideogram spacing

changing ideogram scale

ideogram selection

ideogram order

drawing ideogram regions

chromosome breaks

ordering ideogram regions

cytogenetic bands

drawing multiple genomes

ideogram progression and orientation

relative and absolute ticks

This is the image you will create during this session. It contains chrs 1 & 2 from human and mouse genomes. Each chromosome occupies 1/4 of the figure.

GENOME VISUALIZATION WITH CIRCOS · Session 2 · Ideogram Layout and Formatting

SESSION FINAL IMAGE

2


PUT ON YOUR UNIX HAT

getting ready

3


> cd CIRCOS_FILE_PATH

> cd 2/1

> ls-rw-r--r-- 1 martink users 56728 Apr 30 16:03 circos.pngdrwxr-xr-x 2 martink users 4096 Apr 30 16:03 etc/drwxr-xr-x 2 martink users 4096 Jun 15 2011 img/drwxr-xr-x 2 martink users 4096 Jun 4 2011 misc/

GO TO LESSON DIRECTORY

4


LESSON 1

absolute spacing

5

# 2/1/etc/circos.conf

karyotype = ../data/karyotype.5chr.txt

chromosomes_units = 1000000chromosomes_display_default = yes

<<include ideogram.conf>>

<<include ticks.conf>>

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

<<include etc/colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

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CONFIGURATION FILE

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# 2/data/karyotype.chr5.txt

chr - chr1 1 0 5000000 spectral-5-div-1chr - chr2 2 0 10000000 spectral-5-div-2chr - chr3 3 0 20000000 spectral-5-div-3chr - chr4 4 0 50000000 spectral-5-div-4chr - chr5 5 0 100000000 spectral-5-div-5

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KARYOTYPE FILE

7

> cd 2/1

> circos...created image at ./circos.png

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CREATE CIRCOS IMAGE

8

# 2/1/etc/ideogram.conf

<ideogram>

<spacing>

default = 2u

#default = 10u

#<pairwise chr1 chr2>#spacing = 2u#</pairwise>


</spacing>

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

</ideogram>

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ABSOLUTE SPACING

9


<ideogram>

<spacing>

#default = 2u

default = 10u



</spacing>


</ideogram>

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INCREASE ABSOLUTE SPACING

10


<ideogram>

<spacing>

#default = 2u

default = 10u

<pairwise chr1 chr2>spacing = 2u</pairwise>

<pairwise chr1 chr5>spacing = 25u</pairwise>

</spacing>


</ideogram>

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ADJUST SPACING BETWEEN SPECIFIC IDEOGRAM PAIRS

11


LESSON 2

relative spacing

12


<ideogram>

<spacing>

default = 2u

#default = 0.1r

#<pairwise chr1 chr2>#spacing = 0u # no space#</pairwise>

#<pairwise chr2 chr3>#spacing = 2u # 1Mb space#</pairwise>

#<pairwise chr3 chr4>#spacing = 4u # 2Mb space#</pairwise>

</spacing>


</ideogram>

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ABSOLUTE SPACING

13


<ideogram>

<spacing>

#default = 2u

default = 0.1r

#<pairwise chr1;chr2>#spacing = 0u # no space#</pairwise>

#<pairwise chr2;chr3>#spacing = 2u # 1Mb space#</pairwise>

#<pairwise chr3;chr4>#spacing = 4u # 2Mb space#</pairwise>

</spacing>


</ideogram>

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RELATIVE SPACING

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<ideogram>

<spacing>

#default = 2u

default = 0.1r

<pairwise chr1;chr2>spacing = 0u # no space</pairwise>

<pairwise chr2;chr3>spacing = 2u # 1Mb space</pairwise>

<pairwise chr3;chr4>spacing = 2r # 2x default</pairwise>

</spacing>


</ideogram>

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ABSOLUTE AND RELATIVE SPACING COMBINED

15


LESSON 3

global scale

16


chromosomes_scale = chr1=0.5

#chromosomes_scale = chr1=0.5,chr2=2,chr3=10

# chr1 occupies 50% of figure#chromosomes_scale = chr1=0.5r

# chr5 occupies 25% of figure# chr4 occupies 25% of figure#chromosomes_scale = chr5=0.25r,chr4=0.25r

# chr1 chr2 chr3 together occupy 50% of # figure, and within this region they # are equally sized## equivalent to # chr1=0.0833r,chr2=0.0833r,chr3=0.0833r#chromosomes_scale = /chr[123]/=0.5rn

# all chromosomes equally sized#chromosomes_scale = /./=1rn

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ABSOLUTE IDEOGRAM SCALE

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#chromosomes_scale = chr1=0.5

chromosomes_scale = chr1=0.5,chr2=2,chr3=10





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ABSOLUTE SCALE FOR MULTIPLE IDEOGRAMS

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# chr1 occupies 50% of figurechromosomes_scale = chr1=0.5r




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RELATIVE IDEOGRAM SCALE

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# chr5 occupies 25% of figure# chr4 occupies 25% of figurechromosomes_scale = chr5=0.25r,chr4=0.25r



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RELATIVE SCALE FOR MULTIPLE IDEOGRAMS

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# chr1 chr2 chr3 together occupy 50% of # figure, and within this region they # are equally sized## equivalent to # chr1=0.0833r,chr2=0.0833r,chr3=0.0833rchromosomes_scale = /chr[123]/=0.5rn


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# chr5 occupies 25% of figure# chr4 occupies 25% of figurechromosomes_scale = chr5=0.25r,chr4=0.25r


# all chromosomes equally sizedchromosomes_scale = /./=1rn

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22


LESSON 4

filtering

23


chromosomes_units = 1000000#chromosomes_display_default = yes

chromosomes_display_default = nochromosomes = chr1;chr2;chr3


<ideogram>

<spacing>

default = 2u

#default = 0.01r

</spacing>


</ideogram>

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DRAWING SPECIFIC IDEOGRAMS

24


chromosomes_units = 1000000#chromosomes_display_default = yes

chromosomes_display_default = nochromosomes = chr1;chr2;chr3


<ideogram>

<spacing>

#default = 2u

default = 0.01r

</spacing>


</ideogram>

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RELATIVE SPACING

25


LESSON 5

order

26


# explicitly define orderchromosomes_order = chr1,chr2,chr5,chr4,chr3

# relative order#chromosomes_order = chr3,chr5

# relative order#chromosomes_order = chr1,chr4,-,chr3,chr5

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IDEOGRAM ORDER

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# explicitly define order#chromosomes_order = chr1,chr2,chr5,chr4,chr3

# relative orderchromosomes_order = chr3,chr5

# relative order#chromosomes_order = chr1,chr4,-,chr3,chr5

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IDEOGRAM ORDER

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# explicitly define order#chromosomes_order = chr1,chr2,chr5,chr4,chr3

# relative order#chromosomes_order = chr3,chr5

# relative orderchromosomes_order = chr1,chr4,-,chr3,chr5

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IDEOGRAM ORDER

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LESSON 6

cropping

30


chromosomes = chr5=9-21#chromosomes = chr3=8-12;chr4=4-11;chr5=9-21


<spacing>

default = 0.01rbreak = 0.25r

axis_break = yesaxis_break_at_edge = yesaxis_break_style = 2

<break_style 1>stroke_color = vdgreyfill_color = vdgreythickness = 0.25r</break_style>

<break_style 2>stroke_color = vdgreystroke_thickness = 2thickness = 2r</break_style>

</spacing>

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CROPPING IDEOGRAMS

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chromosomes = chr5=9-21#chromosomes = chr3=8-12;chr4=4-11;chr5=9-21


<spacing>





</spacing>

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CROPPING IDEOGRAMS

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#chromosomes = chr5=9-21chromosomes = chr3=8-12;chr4=4-11;chr5=9-21

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CROPPING IDEOGRAMS

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LESSON 7

axis breaks

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chromosomes_breaks = -chr5=11-19#chromosomes_breaks = -chr3=13-17; -chr4=(-9;-chr4=41-);

-chr5=11-19


<spacing>





</spacing>

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IDEOGRAM BREAKS

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#chromosomes_breaks = -chr5=11-19chromosomes_breaks = -chr3=13-17; -chr4=(-9;-chr4=41-);

-chr5=11-19


<spacing>





</spacing>

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IDEOGRAM BREAKS

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LESSON 8

ordering cropped regions

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chromosomes = chr3:0-11; chr4[4a]:0-11; chr4[4b]:19-31; chr5[5a]:9-21; chr5[5b]:29-41;

chromosomes_order = ^,chr1,4a,chr3,4b,-,5b,5a

#chromosomes_scale = 5a=2,5b=2

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ORDERING CROPPED IDEOGRAMS

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chromosomes = chr3:0-11; chr4[4a]:0-11; chr4[4b]:19-31; chr5[5a]:9-21; chr5[5b]:29-41;

chromosomes_order = ^,chr1,4a,chr3,4b,-,5b,5a

chromosomes_scale = 5a=2,5b=2

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ORDERING AND SCALING CROPPED IDEOGRAMS

39


LESSON 9

cytogenetic bands

40

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CYTOGENETIC BANDS IN BROWSERS

41

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CONVENTIONAL BAND COLOR SCHEME

42


karyotype = ../data/karyotype.5chr.banded.txt

# 2/data/karyotype.5chr.banded.txt

band chr1 band1 band1 0 2500000 gnegband chr1 band2 band2 2500000 5000000 gpos25

band chr2 band1 band1 0 2500000 gnegband chr2 band2 band2 2500000 5000000 gpos25band chr2 band3 band3 5000000 7500000 gpos100band chr2 band4 band4 7500000 10000000 gvar

# 2/9/ideogram.conf

<<include ../../etc/ideogram.conf>>band_transparency* = 0

# 2/etc/ideogram.conf

show_bands = yesfill_bands = yesband_stroke_thickness = 1band_transparency = 1

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DEFINING AND DRAWING BANDS

43


karyotype = ../data/karyotype.5chr.banded.txt

# 2/data/karyotype.5chr.banded.txt

band chr1 band1 band1 0 2500000 gnegband chr1 band2 band2 2500000 5000000 gpos25

band chr2 band1 band1 0 2500000 gnegband chr2 band2 band2 2500000 5000000 gpos25band chr2 band3 band3 5000000 7500000 gpos100band chr2 band4 band4 7500000 10000000 gvar

# 2/9/ideogram.conf

<<include ../../etc/ideogram.conf>>band_transparency* = 4

# 2/etc/ideogram.conf

show_bands = yesfill_bands = yesband_stroke_thickness = 1band_transparency = 1

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DEFINING AND DRAWING BANDS

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LESSON 10

whole genome karyotypes

45


karyotype = data/karyotype/ karyotype.human.txt

#karyotype = data/karyotype/ karyotype.mouse.txt

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

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HUMAN GENOME IDEOGRAMS

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# UCSC genome browser RGB # colors for human chromosomeschr1 = 153,102,0chr2 = 102,102,0chr3 = 153,153,30chr4 = 204,0,0chr5 = 255,0,0chr6 = 255,0,204chr7 = 255,204,204chr8 = 255,153,0chr9 = 255,204,0chr10 = 255,255,0chr11 = 204,255,0chr12 = 0,255,0chr13 = 53,128,0...chr21 = 204,153,255chr22 = 102,102,102chr23 = 153,153,153chrX = 153,153,153chr24 = 204,204,204chrY = 204,204,204chrM = 204,204,153chr0 = 204,204,153chrUn = 121,204,61chrNA = 255,255,255

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CONVENTIONAL IDEOGRAM COLOR SCHEME

47


#karyotype = ../../data/karyotype/ karyotype.human.txt

karyotype = ../../data/karyotype/ karyotype.mouse.txt

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

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MOUSE GENOME IDEOGRAMS

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# data/karyotype/karyotype.human.hg19.txt

chr - hs1 hs1 0 249250621 chr1chr - hs2 hs2 0 243199373 chr2chr - hs3 hs3 0 198022430 chr3chr - hs4 hs4 0 191154276 chr4chr - hs5 hs5 0 180915260 chr5chr - hs6 hs6 0 171115067 chr6chr - hs7 hs7 0 159138663 chr7chr - hs8 hs8 0 146364022 chr8chr - hs9 hs9 0 141213431 chr9chr - hs10 hs10 0 135534747 chr10chr - hs11 hs11 0 135006516 chr11chr - hs12 hs12 0 133851895 chr12chr - hs13 hs13 0 115169878 chr13chr - hs14 hs14 0 107349540 chr14chr - hs15 hs15 0 102531392 chr15chr - hs16 hs16 0 90354753 chr16chr - hs17 hs17 0 81195210 chr17chr - hs18 hs18 0 78077248 chr18chr - hs19 hs19 0 59128983 chr19chr - hs20 hs20 0 63025520 chr20chr - hs21 hs21 0 48129895 chr21chr - hs22 hs22 0 51304566 chr22chr - hsx hsx 0 155270560 chrxchr - hsy hsy 0 59373566 chry

HG & MM KARYOTYPE DEFINITIONS# data/karyotype/karyotype.mouse.mm9.txt

chr - mm1 mm1 0 197195432 whitechr - mm2 mm2 0 181748087 whitechr - mm3 mm3 0 159599783 whitechr - mm4 mm4 0 155630120 whitechr - mm5 mm5 0 152537259 whitechr - mm6 mm6 0 149517037 whitechr - mm7 mm7 0 152524553 whitechr - mm8 mm8 0 131738871 whitechr - mm9 mm9 0 124076172 whitechr - mm10 mm10 0 129993255 whitechr - mm11 mm11 0 121843856 whitechr - mm12 mm12 0 121257530 whitechr - mm13 mm13 0 120284312 whitechr - mm14 mm14 0 125194864 whitechr - mm15 mm15 0 103494974 whitechr - mm16 mm16 0 98319150 whitechr - mm17 mm17 0 95272651 whitechr - mm18 mm18 0 90772031 whitechr - mm19 mm19 0 61342430 whitechr - mmx mmx 0 166650296 whitechr - mmy mmy 0 15902555 white

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#karyotype = ../../data/karyotype/ karyotype.mouse.txt

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

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DRAWING MULTIPLE KARYOTYPES

50



#karyotype = ../../data/karyotype/ karyotype.mouse.txt

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


thickness* = 10pstroke_thickness* = 0

<spacing>default = 0.01r</spacing>

# 2/10/etc/ticks.conf

<tick>spacing = 20usize = 8pthickness = 2p</tick>

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#karyotype = ../../data/karyotype/ karyotype.human.hg19.txt

#karyotype = ../../data/karyotype/ karyotype.mouse.mm9.txt

karyotype = ../../data/karyotype/ karyotype.human.hg19.txt, ../../data/karyotype/ karyotype.mouse.mm9.txt


thickness* = 10pstroke_thickness* = 0

<spacing>default = 0.01r</spacing>


<tick>spacing = 50usize = 8pthickness = 1p</tick>

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52

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GENOME.UCSC.EDU

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#chr chrStart chrEnd name gieStainchr1 0 2300000 p36.33 gnegchr1 2300000 5400000 p36.32 gpos25chr1 5400000 7200000 p36.31 gnegchr1 7200000 9200000 p36.23 gpos25chr1 9200000 12700000 p36.22 gnegchr1 12700000 16200000 p36.21 gpos50chr1 16200000 20400000 p36.13 gnegchr1 20400000 23900000 p36.12 gpos25chr1 23900000 28000000 p36.11 gnegchr1 28000000 30200000 p35.3 gpos25chr1 30200000 32400000 p35.2 gneg...chr1 227000000 230700000 q42.13 gnegchr1 230700000 234700000 q42.2 gpos50chr1 234700000 236600000 q42.3 gnegchr1 236600000 243700000 q43 gpos75chr1 243700000 249250621 q44 gnegchr2 0 4400000 p25.3 gnegchr2 4400000 7100000 p25.2 gpos50chr2 7100000 12200000 p25.1 gnegchr2 12200000 16700000 p24.3 gpos75chr2 16700000 19200000 p24.2 gnegchr2 19200000 24000000 p24.1 gpos75...

UCSC KARYOTYPE TABLE

54


# from lesson 10 directory

> pwdCIRCOS_FILE_PATH/2/10> cd ../../data

# now in course’s data directory

> cd karyotype

> ls

-rw-r--r-- 1 martink users 40154 Jun 11 11:37 karyotype.human.hg19.txt-rw-r--r-- 1 martink users 30795 Jun 15 10:44 karyotype.human.ucscraw.txt-rw-r--r-- 1 martink users 17852 Jun 11 11:37 karyotype.mouse.mm9.txt-rw-r--r-- 1 martink users 10644 Jun 14 13:27 karyotype.rat.rn4.txt-rwxr-xr-x 1 martink users 1045 Jun 15 10:59 parse.karyotype

> ./parse.karyotype karyotype.human.ucscraw.txt hs# 1. chromosomeschr - hsx x 0 q28 chrxchr - hsy y 0 q12 chrychr - hs1 1 0 q44 chr1chr - hs2 2 0 q37.3 chr2chr - hs3 3 0 q29 chr3chr - hs4 4 0 q35.2 chr4chr - hs5 5 0 q35.3 chr5...

PARSING UCSC KARYOTYPE TABLES

55


LESSON 11

regex filtering, color, progression & orientation

56


# all ideograms displayed, # except hs1, hs2, mm1, mm2chromosomes_display_default = yeschromosomes = -hs1;-hs2;-mm1;-mm2

# all ideograms displayed, except# those matching regular expression [xy]#chromosomes_display_default = yes#chromosomes = -/[xy]/

# all ideograms displayed, except # hs1, hs2 and those those matching # regular expressions y or \d\d#chromosomes_display_default = yes#chromosomes = -hs1;-hs2;-/y/;-/\d\d/;

# only the specified ideograms displayed: # hs1-hs5, hs10, mm10-mm15, mmx#chromosomes_display_default = no#chromosomes = /hs[1-5]$/;hs10;/mm1[0-5]/;mmx

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IDEOGRAM REGEX FILTERING

57


# all ideograms displayed, # except hs1, hs2, mm1, mm2#chromosomes_display_default = yes#chromosomes = -hs1;-hs2;-mm1;-mm2

# all ideograms displayed, except# those matching regular expression [xy]chromosomes_display_default = yeschromosomes = -/[xy]/



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58




# all ideograms displayed, except # hs1, hs2 and those those matching # regular expressions y or \d\dchromosomes_display_default = yeschromosomes = -hs1;-hs2;-/y/;-/\d\d/;


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59





# only the specified ideograms displayed: # hs1-hs5, hs10, mm10-mm15, mmxchromosomes_display_default = nochromosomes = /hs[1-5]$/;hs10;/mm1[0-5]/;mmx

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60

# 2/11/etc/circos.conf# human chromosomes: red # mouse chromosomes: blue# mouse chromosomes are reversedchromosomes_display_default = yeschromosomes_color = /hs/=reds-5-seq-5, /mm/=blues-5-seq-5chromosomes_reverse = /mm/

# only human chromosomes are shown, # each occupying 1/24th of the image#chromosomes_display_default = no#chromosomes = /hs/#chromosomes_scale = /hs/=1rn

# 5 human (hs1...hs5) and 3 mouse # (mm17...mm19) chromosomes are shown# human chromosomes occupy 50% # of the image (each occupies 10%)# mouse chromosomes occupy 50% # of the image (each occupies 16.7%)#chromosomes_display_default = no#chromosomes = /hs[1-5]$/;/mm1[7-9]/#chromosomes_scale = /hs/=0.5rn,/mm/=0.5rn

#chromosomes_display_default = no#chromosomes = hs1;hs2;mm1;mm2#chromosomes_order = hs1,hs2,mm2,mm1#chromosomes_reverse = /mm/#chromosomes_scale = /./=1rn#chromosomes_color = hs1:rdylbu-11-div-2, hs2:rdylbu-11-div-3, mm1:rdylbu-11-div-10, mm2:rdylbu-11-div-9

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COLOR, PROGRESSION & ORIENTATION

61

# 2/11/etc/circos.conf# human chromosomes: red # mouse chromosomes: blue# mouse chromosomes are reversed#chromosomes_display_default = yes#chromosomes_color = /hs/=reds-5-seq-5, /mm/=blues-5-seq-5#chromosomes_reverse = /mm/

# only human chromosomes are shown, # each occupying 1/24th of the imagechromosomes_display_default = nochromosomes = /hs/chromosomes_scale = /hs/=1rn



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62



# 5 human (hs1...hs5) and 3 mouse # (mm17...mm19) chromosomes are shown# human chromosomes occupy 50% # of the image (each occupies 10%)# mouse chromosomes occupy 50% # of the image (each occupies 16.7%)chromosomes_display_default = nochromosomes = /hs[1-5]$/;/mm1[7-9]/chromosomes_scale = /hs/=0.5rn,/mm/=0.5rn


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63




chromosomes_display_default = nochromosomes = hs1;hs2;mm1;mm2chromosomes_order = hs1,hs2,mm2,mm1chromosomes_reverse = /mm/chromosomes_scale = /./=1rnchromosomes_color = hs1:rdylbu-11-div-2, hs2:rdylbu-11-div-3, mm1:rdylbu-11-div-10, mm2:rdylbu-11-div-9

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64


LESSON 12

ticks & grids

65


chromosomes_display_default = no

chromosomes = hs1;hs2;mm1;mm2chromosomes_order = hs1,hs2,mm2,mm1chromosomes_color = hs1=rdylbu-11-div-2, hs2=rdylbu-11-div-3, mm1=rdylbu-11-div-10, mm2=rdylbu-11-div-9

chromosomes_reverse = mm1,mm2chromosomes_scale = /./=0.25r

<highlights><highlight>file = ../data/highlight.txtr0 = 1r+40pr1 = 1r+45p</highlight></highlights>


show_ticks = noshow_tick_labels = noshow_grid = no

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TICKS AND GRIDS

66


show_ticks = yes

<ticks>radius = dims(ideogram,radius_outer) + 45pcolor = black...

# absolute tick groups

<tick>spacing = 20usize = 12pthickness = 2p...</tick>



...

</ticks>.


TICKS AND GRIDS

67


...

# relative tick groups

<tick>radius = 0.75rspacing_type = relativerspacing = 0.02size = 3pthickness = 1p</tick>

<tick>radius = 0.75rspacing_type = relativerspacing = 0.10size = 6pthickness = 1p</tick>

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TICKS AND GRIDS

68


show_ticks = yesshow_tick_labels = yesshow_grid = no

<ticks>tick_label_font = lightlabel_offset = 5plabel_size = 8pmultiplier = 1e-6...

<tick>spacing = 20usize = 12pthickness = 2pshow_label = yeslabel_size = 10pformat = %d</tick>

...

</ticks>

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TICKS AND GRIDS

69


show_ticks = yesshow_tick_labels = yesshow_grid = yes

<ticks>...

<tick>spacing = 20u...grid_start = 1rgrid_end = 1r+45pgrid_color = vdgreygrid_thickness = 1pgrid = yes</tick>

...

</ticks>

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TICKS AND GRIDS

70

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Documents

ideogram layout and formatting - mkweb.bcgsc.camkweb.bcgsc.ca/dev/circos/documentation/course/slides/session-2.pdf · GENOME VISUALIZATION WITH CIRCOS · Session 2 · Ideogram Layout