IDEOGRAM LAYOUT GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 1 - - PowerPoint PPT Presentation

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca

IDEOGRAM LAYOUT

SESSION 2

1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca

drawing and spacing ideograms relative ideogram spacing changing ideogram scale ideogram selection ideogram order drawing ideogram regions chromosome breaks

• rdering ideogram regions

cytogenetic bands drawing multiple genomes ideogram progression and orientation relative and absolute ticks

2

SESSION PLAN

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca

This is the image you will create during this session. The figure uses ideogram selection, ordering, scale reversal, global scaling, highlights, grids and absolute and relative tick marks.

3

FINAL FIGURE

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 4

LESSON 1

DRAWING IDEOGRAMS

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 5

!"#$"%&#'(#)*&*+**'),*&-&." !"/*" +0# "1'*# "*-2.34,5"

SWITCH TO SESSION 2 LESSON 1 DIRECTORY 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 6

The 67(8)084+ parameter is used to specify the file that defines the chromosome number and size for the genome (or genomes) to be drawn.

99',#/:$+"'$+)5(713#),;!!"" 99',#/:$+"0'#6*3#),;!!" 9'175+!" ;'/+"<"*-2.34,5" 99',#/:$+"33&+0#&'175+3#),;!!" 9&'175+!" !"#$%&$'()*)++,-"&",!"#$%&$'(+&.&" #=()1)*)1+*>:,'0*"""""""""""<".??????" #=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" 99',#/:$+"33&33&+0#&=):*+6++4',53#),;!!"

*+**'),*&-&+0#&#'(#)*3#),;"

CONFIGURATION FILE 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 7

The last field is the color. Color names @AB2, correspond to a Brewer palette.

C";'(*0"0D)";'+/$*"E#=("2F"7(+"(+A:'(+$G";)//)D+$"@8" C"#=()1)*)1+",71+"E#=(-F" C"#=()1)*)1+"/7@+/"E-F" C"#=()1)*)1+"*07(0"E?F" C"#=()1)*)1+"+,$"EH??????F" C"#=()1)*)1+"#)/)("E@A.2.F" #=("2"#=(."."?"""H??????"@A.2." #=("2"#=(-"-"?"".???????"@A.2-" #=("2"#=(I"I"?""-???????"@A.2I" #=("2"#=(J"J"?""H???????"@A.2J" #=("2"#=(H"H"?".????????"@A.2H"

*+**'),*&-&$707&67(8)084+30K0"

KARYOTYPE FILE 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 8

A 5-color qualitative Brewer palette. For other schemes, see www.colorbrewer.org!

C"@LB2," C"L<A"M"A:7/'070'N+" C"L<$"M"$'N+(5+,0" C"L<*"M"*+A:+,0'7/" C"B"""M"47/+00+"',$+K" C","""M"#)/)("',$+K"',"47/+00+"" C"H"#)/)("A:7/'070'N+G"47*0+/"." @A.2."<"-H.G.O?G.PJ" @A.2-"<".PQG-?HG--P" @A.2I"<"-?JG-IHG.QP" @A.2J"<"---G-?IG--O" @A.2H"<"-HJG-.PG.RR" C"I"#)/)("*+A:+,0'7/G"8+//)D25(++,2@/:+" @*O2."<"-IPG-JOG.PP" @*O2-"<".-PG-?HG.OP" @*O2I"<"JJG.-PG.OJ"

*+**'),*&+0#&@(+D+(3#),;"

BREWER PALETTES 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 9

Five ideograms, arranged clockwise from 12 o’clock.!

9'$+)5(71!" 9*47#',5!" $+;7:/0"<"-:" C$+;7:/0"<".?:" C947'(D'*+"#=(.S#=(-!" C*47#',5"<"-:" C9&47'(D'*+!" C947'(D'*+"#=(HS#=(.!" C*47#',5"<"-H:" C9&47'(D'*+!"

*+**'),*&-&.&+0#&'$+)5(713#),;"

FIXED ABSOLUTE SPACING 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 10

Five ideograms, arranged clockwise from 12 o’clock.!

!"#$"%&#'(#)*&*+**'),*&-&." !"(:,#'(#)*" 333" #(+70+$"'175+"70"3&*-2.34,5"

FIXED ABSOLUTE SPACING 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 11

Changing the spacing from 2u to 10u has increased spacing by 5- fold.!

9'$+)5(71!" 9*47#',5!" C$+;7:/0"<"-:" $+;7:/0"<".?:" C947'(D'*+"#=(.S#=(-!" C*47#',5"<"-:" C9&47'(D'*+!" C947'(D'*+"#=(HS#=(.!" C*47#',5"<"-H:" C9&47'(D'*+!"

*+**'),*&-&.&+0#&'$+)5(713#),;"

INCREASING SPACING 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 12

Spacing between individual ideogram pairs can be adjusted

• independently. This is done using the 947'(D'*+!"block.!

9'$+)5(71!" 9*47#',5!" C$+;7:/0"<"-:" $+;7:/0"<".?:" 947'(D'*+"#=(.S#=(-!" *47#',5"<"-:" 9&47'(D'*+!" C947'(D'*+"#=(HS#=(.!" C*47#',5"<"-H:" C9&47'(D'*+!"

*+**'),*&-&.&+0#&'$+)5(713#),;"

CHANGING SPACING BETWEEN PAIRS 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 13

Two 947'(D'*+! blocks are used to decrease the spacing between chromosomes 1 and 2 to 2u and increase the spacing between chromosomes 5 and 1 to 25u.!

9'$+)5(71!" 9*47#',5!" C$+;7:/0"<"-:" $+;7:/0"<".?:" 947'(D'*+"#=(.S#=(-!" *47#',5"<"-:" 9&47'(D'*+!" 947'(D'*+"#=(HS#=(.!" *47#',5"<"-H:" 9&47'(D'*+!"

*+**'),*&-&.&+0#&'$+)5(713#),;"

CHANGING SPACING BETWEEN PAIRS 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 14

LESSON 2

RELATIVE SPACING

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 15

!"#$"%&#'(#)*&*+**'),*&-&-" !"/*" +0# "*-2-34,5"

SWITCH TO SESSION 2 LESSON 2 DIRECTORY 1

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 16

Ideogram spacing can be made relative to total ideogram size by using the r suffix. For example, the block below sets each space to 10% of total ideogram size.!

9'$+)5(71!" 9*47#',5!" C$+;7:/0"<"-:" C"T=+,"*47#',5":,'0"'*"U(UG"" C"0=+";(7#0'),"'*"#7/#:/70+$" C"(+/70'N+"0)"0=+"0)07/"*'V+");"7//" '$+)5(71*3"" C"+353"';"7//"'$+)5(71*"0)07/".OH"W@G"" C"?3.("*47#',5"'*".O3HW@" $+;7:/0"<"?3.("

*+**'),*&-&-&+0#&'$+)5(713#),;"

RELATIVE SPACING 2

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 17

Absolute and relative spacing can be used in the same figure. Here, default ideogram spacing is relative (0.1r), but spacing between the first four chromosomes is set to 0u, 1u and 2u, respectively.!

9'$+)5(71!" 9*47#',5!" $+;7:/0"<"?3.(" 947'(D'*+"#=(.S#=(-!" *47#',5"<"?:"C",)"*47#+"" 9&47'(D'*+!" 947'(D'*+"#=(-S#=(I!" *47#',5"<".:"C".W@"*47#+" 9&47'(D'*+!" 947'(D'*+"#=(IS#=(J!" *47#',5"<"-:"C"-W@"*47#+" 9&47'(D'*+!" 9&*47#',5!"

*+**'),*&-&-&+0#&'$+)5(713#),;"

ABSOLUTE AND RELATIVE SPACING 2

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 18

LESSON 3

IDEOGRAM SCALE

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 19

By changing the scale of chromosome 1 to 0.5x using the chromosomes_scale parameter, the ideogram of this chromosome is shrunk by 2x.!

99',#/:$+"'$+)5(713#),;!!" 99',#/:$+"0'#6*3#),;!!" 9'175+!" ;'/+"<"*-2I34,5" 99',#/:$+"33&+0#&'175+3#),;!!" 9&'175+!" 67(8)084+"<"33&$707&67(8)084+30K0" #=()1)*)1+*>:,'0*"""""""""""<".??????" #=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" #=()1)*)1+*>*#7/+"<"#=(.X?3H" C#=()1)*)1+*>*#7/+"<"#=(.X?3HS#=(-X-S#=(IX.?" C"#=(.")##:4'+*"H?Y");";'5:(+" C#=()1)*)1+*>*#7/+"<"#=(.XIO" C"#=(.")##:4'+*"PHY");";'5:(+" C#=()1)*)1+*>*#7/+"<"#=(.X..J"

*+**'),*&-&I&+0#&#'(#)*3#),;"

GLOBAL IDEOGRAM SCALE 3

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 20

By changing the scale of chromosome 1 to 0.5x, chromosome 2 to 2x and chromosome 3 to 10x, the figure’s focus shifts to chromosome 3 (which is now magnified 10x) and away from chromosome 1 (which is reduced 2x).!

99',#/:$+"'$+)5(713#),;!!" 99',#/:$+"0'#6*3#),;!!" 9'175+!" ;'/+"<"*-2I34,5" 99',#/:$+"33&+0#&'175+3#),;!!" 9&'175+!" 67(8)084+"<"33&$707&67(8)084+30K0" #=()1)*)1+*>:,'0*"""""""""""<".??????" #=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" #=()1)*)1+*>*#7/+"<"#=(.X?3H" #=()1)*)1+*>*#7/+"<"#=(.X?3HS#=(-X-S#=(IX.?" C"#=(.")##:4'+*"H?Y");";'5:(+" C#=()1)*)1+*>*#7/+"<"#=(.XIO" C"#=(.")##:4'+*"PHY");";'5:(+" C#=()1)*)1+*>*#7/+"<"#=(.X..J"

*+**'),*&-&I&+0#&#'(#)*3#),;"

GLOBAL IDEOGRAM SCALE 3

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 21

#=()1)*)1+*>*#7/+"<"#=(.XIO"

By changing the scale of chr1 to 38, it is made to occupy 50% of the figure.

#=()1)*)1+*>*#7/+"<"#=(.X..J"

By changing the scale of chr1 to 114, it is made to occupy 75% of the figure.

FITTING IDEOGRAMS TO FRACTION OF IMAGE 3

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 22

LESSON 4

IDEOGRAM SELECTION

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 23

By turning off default chromosome display and setting the chromosomes parameter, you can control which chromosomes are drawn.!

C#=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" #=()1)*)1+*>$'*4/78>$+;7:/0"<",)" #=()1)*)1+*"<"#=(.S#=(-S#=(I"

*+**'),*&-&J&+0#&#'(#)*3#),;"

SELECTING IDEOGRAMS FOR DISPLAY 4

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 24

When ideogram spacing is set to relative, the fraction of the ideogram circle occupied by spaces is the same regardless of the total ideogram size. left Spacing is set to 0.01r and the total ideogram size is 35Mb. right Spacing is also 1u but ideogram size is 185Mb.

BENEFIT OF RELATIVE SPACING 4

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 25

LESSON 5

IDEOGRAM ORDER

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 26

Ideogram order can be adjusted using #=()1)*)1+*>)($+(.!

#=()1)*)1+*>:,'0*"""""""""""<".??????" #=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" C"+K4/'#'0/8"$+;',+")($+(" #=()1)*)1+*>)($+("<"#=(.G#=(-G#=(HG#=(JG#=(I" C"(+/70'N+")($+(" C#=()1)*)1+*>)($+("<"#=(IG#=(H" C"(+/70'N+")($+(" C#=()1)*)1+*>)($+("<"#=(.G#=(JG2G#=(IG#=(H" 99',#/:$+"33&+0#&=):*+6++4',53#),;!!"

*+**'),*&-&H&+0#&#'(#)*3#),;"

ORDERING IDEOGRAMS 5

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 27

To change the order of a subset of ideograms, set #=()1)*)1+*>)($+( to the order of the subset. You do not need to specify the order of the full set.!

#=()1)*)1+*>:,'0*"""""""""""<".??????" #=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" C"+K4/'#'0/8"$+;',+")($+(" C#=()1)*)1+*>)($+("<" #=(.G#=(-G#=(HG#=(JG#=(I" C"(+/70'N+")($+(" #=()1)*)1+*>)($+("<"#=(IG#=(H" C"(+/70'N+")($+(" C#=()1)*)1+*>)($+("<"#=(.G#=(JG2G#=(IG#=(H" 99',#/:$+"33&+0#&=):*+6++4',53#),;!!"

*+**'),*&-&H&+0#&#'(#)*"

ORDERING IDEOGRAM SUBSET 5

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 28

To change the order of a several ideogram subsets, separate the

• rder of subsets by a “2“ in #=()1)*)1+*>)($+(.!

#=()1)*)1+*>:,'0*"""""""""""<".??????" #=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" C"+K4/'#'0/8"$+;',+")($+(" C#=()1)*)1+*>)($+("<" #=(.G#=(-G#=(HG#=(JG#=(I" C"(+/70'N+")($+(" C#=()1)*)1+*>)($+("<"#=(IG#=(H" C"(+/70'N+")($+(" #=()1)*)1+*>)($+("<"#=(.G#=(JG2G#=(IG#=(H" 99',#/:$+"33&+0#&=):*+6++4',53#),;!!"

*+**'),*&-&H&+0#&#'(#)*3#),;"

ORDERING MULTIPLE IDEOGRAM SUBSETS 5

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 29

LESSON 6

IDEOGRAM REGIONS

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 30

Ideograms can be cropped by using the chromosomes parameter. Here, ideogram of chromosome 5 cropped to the 9-21 Mb region.!

#=()1)*)1+*>:,'0*"""""""""""<".??????" #=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" #=()1)*)1+*""<"#=(HXQ2-."

*+**'),*&-&R&+0#&#'(#)*3#),;"

CROPPING IDEOGRAMS 6

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 31

Multiple ideograms can be cropped. Here ideograms are cropped to chr3:8-12, chr4:4-11, chr5:9-21.!

#=()1)*)1+*"<"#=(IXO2.-S#=(JXJ2..S#=(HXQ2-."

*+**'),*&-&R&+0#&#'(#)*3#),;"

CROPPING MULTIPLE IDEOGRAMS 6

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 32

LESSON 7

CHROMOSOME BREAKS

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 33

Regions of chromosomes can be removed from the display by using #=()1)*)1+*>@(+76*. In this figure region chr5: 11-19 Mb is removed and replaced by an axis break.!

#=()1)*)1+*>@(+76*""<"2#=(HX..2.Q"

*+**'),*&-&P&+0#&#'(#)*3#),;"

AXIS BREAKS 7

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 34

Multiple breaks are defined. Regions removed are! chr3:13-17, chr4:start-9, chr4:41-end, chr5:11-19!

#=()1)*)1+*>@(+76*""<"" ""2#=(IX.I2.PS2#=(JXE2QS2#=(JXJ.2FS" ""2#=(HX..2.Q"

*+**'),*&-&P&+0#&#'(#)*3#),;"

MULTIPLE AXIS BREAKS 7

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 35

LESSON 8

ORDERING REGIONS

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 36

A chromosome can be split into multiple, independently ordered ideograms by using tags in the chromosomes parameter to associate a unique name to each ideogram. Chromosome 4 is split into two pieces (a and b) which correspond to 0-11 Mb and 19-31 Mb of the chromosome.!

#=()1)*)1+*"""""""<"" ""#=(IX?2..S#=(JZ7[X?2..S#=(JZ@[X.Q2I." #=()1)*)1+*>)($+("<"\G#=(.G7G#=(IG@"

*+**'),*&-&O&+0#&#'(#)*3#),;"

REORDERING IDEOGRAM SEGMENTS 8

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 37

LESSON 9

CYTOGENETIC BANDS

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca

Views showing cytogenetic bands in UCSC and Ensembl browsers (same band position is indicated by a red arrow).

38

CYTOGENETIC BANDS 9

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca

Band colors are defined in color.conf to correspond to the color scheme of the UCSC genome browser and the names given to the bands in the UCSC Karyotype table. For example, acen is used for centromeres, typically shown in red.

39

CYTOGENETIC BAND COLORS 9

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 40

Bands are defined together with chromosomes in the karyotype file. The syntax for a band is the same as for a chromosome, except that the line starts with “band” and the second field now defines the parent chromosome.

C"0=+";'(*0";'+/$"1:*0"@+"]@7,$^" C"0=+"*+#),$";'+/$"'*"0=+"@7,$_*"#=()1)*)1+"" C"0=+",+K0"0D)";'+/$*"7(+"0=+",71+"7,$"" C"/7@+/");"0=+"@7,$"E,)0":*+$G"@:0"1:*0"@+"4(+*+,0F" C"0=+"/7*0"0=(++";'+/$*"7(+"0=+"*07(0G"" C"+,$"7,$"#)/)(");"0=+"@7,$3" @7,$"#=(."@7,$."@7,$."?"-H?????"5,+5" @7,$"#=(."@7,$-"@7,$-"-H?????"H??????"54)*-H" @7,$"#=(-"@7,$."@7,$."?"-H?????"5,+5" @7,$"#=(-"@7,$-"@7,$-"-H?????"H??????"54)*-H" @7,$"#=(-"@7,$I"@7,$I"H??????"PH?????"54)*.??" @7,$"#=(-"@7,$J"@7,$J"PH?????".???????"5N7(" @7,$"#=(I"@7,$."@7,$."?".??????"*07/6" @7,$"#=(I"@7,$-"@7,$-".??????"H??????"54)*H?" @7,$"#=(I"@7,$I"@7,$I"H??????"PH?????"54)*.??" @7,$"#=(I"@7,$J"@7,$J"PH?????".???????"5N7(" @7,$"#=(I"@7,$H"@7,$H".???????".H??????"7#+," @7,$"#=(I"@7,$P"@7,$P".H??????".Q??????"5,+5" @7,$"#=(I"@7,$O"@7,$O".Q??????"-???????"*07/67"

*+**'),*&-&$707&67(8)084+3@7,$+$30K0"

CYTOGENETIC BAND DEFINITION 9

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 41

Cytogenetic bands appear as stripes within the ideogram segment.!

@7,$"#=(."@7,$."@7,$."?"-H?????"5,+5" @7,$"#=(."@7,$-"@7,$-"-H?????"H??????"54)*-H" @7,$"#=(-"@7,$."@7,$."?"-H?????"5,+5" @7,$"#=(-"@7,$-"@7,$-"-H?????"H??????"54)*-H" @7,$"#=(-"@7,$I"@7,$I"H??????"PH?????"54)*.??" @7,$"#=(-"@7,$J"@7,$J"PH?????".???????"5N7(" @7,$"#=(I"@7,$."@7,$."?".??????"*07/6" @7,$"#=(I"@7,$-"@7,$-".??????"H??????"54)*H?" @7,$"#=(I"@7,$I"@7,$I"H??????"PH?????"54)*.??" @7,$"#=(I"@7,$J"@7,$J"PH?????".???????"5N7(" @7,$"#=(I"@7,$H"@7,$H".???????".H??????"7#+," @7,$"#=(I"@7,$P"@7,$P".H??????".Q??????"5,+5" @7,$"#=(I"@7,$O"@7,$O".Q??????"-???????"*07/6"

*+**'),*&-&$707&67(8)084+3@7,$+$30K0"

CYTOGENETIC BANDS 9

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 42

By changing @7,$>0(7,*47(+,#8 in the 9'$+)5(71! block, the band pattern can be made semi-transparent to allow the color of the ideogram to show through. Using this parameter you can combine the ideogram color and the band pattern.!

@7,$>0(7,*47(+,#8"<"I"

*+**'),*&-&Q&+0#&'$+)5(713#),;"

ADDING TRANSPARENCY TO BANDS 9

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 43

LESSON 10

MULTIPLE GENOMES

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 44

You can download karyotype definitions from UCSC Genome Browser table viewer (karyotype table).

#=("2"=*."."?"-JP-JQP.Q"#=(." #=("2"=*-"-"?"-J-QH..JQ"#=(-" #=("2"=*I"I"?".QQH?.O-P"#=(I" #=("2"=*J"J"?".Q.-PI?RI"#=(J" #=("2"=*H"H"?".O?OHPORR"#=(H" #=("2"=*R"R"?".P?OQQQQ-"#=(R" #=("2"=*P"P"?".HOO-.J-J"#=(P" 333" #=("2"11."."?".QP.QHJI-"D='0+" #=("2"11-"-"?".O.PJO?OP"D='0+" #=("2"11I"I"?".HQHQQPOI"D='0+" #=("2"11J"J"?".HHRI?.-?"D='0+" #=("2"11H"H"?".H-HIP-HQ"D='0+" #=("2"11R"R"?".JQH.P?IP"D='0+" #=("2"11P"P"?".H-H-JHHI"D='0+" 33"

*+**'),*&-&$707&67(8)084+3=:17,30K0"

HUMAN GENOME KARYOTYPE 10

*+**'),*&-&$707&67(8)084+31):*+30K0"

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 45

All chromosomes in the human genome. The figure uses the human karyotype file which defines 24 chromosomes (1..22, X, Y) and the cytogenetic bands. Bands are drawn with transparency.!

67(8)084+"<"33&$707&67(8)084+3=:17,30K0" C67(8)084+"<"33&$707&67(8)084+31):*+30K0" C67(8)084+"<"33&$707& 67(8)084+3=:17,>1):*+30K0" C67(8)084+"<"33&$707& 67(8)084+3=:17,>1):*+>/7@+/*30K0"

*+**'),*&-&.?&+0#&#'(#)*3#),;"

DRAWING THE HUMAN GENOME 10

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 46

Conventional color palette for the human genome used by the UCSC genome browser. These colors are defined in the #)/)(3#),; file, named after the chromosome name, but with a “chr” prefix (e.g. hs1 has color chr1).!

C"`aba"5+,)1+"@()D*+("cde"" C"#)/)(*";)("=:17,"#=()1)*)1+*" #=(."<".HIG.?-G?" #=(-"<".?-G.?-G?" #=(I"<".HIG.HIGI?" #=(J"<"-?JG?G?" #=(H"<"-HHG?G?" #=(R"<"-HHG?G-?J" #=(P"<"-HHG-?JG-?J" #=(O"<"-HHG.HIG?" #=(Q"<"-HHG-?JG?" #=(.?"<"-HHG-HHG?" #=(.."<"-?JG-HHG?" #=(.-"<"?G-HHG?" #=(.I"<"HIG.-OG?" 333" #=(-."<"-?JG.HIG-HH" #=(--"<".?-G.?-G.?-" #=(-I"<".HIG.HIG.HI" #=(L""<".HIG.HIG.HI" #=(-J"<"-?JG-?JG-?J" #=(f""<"-?JG-?JG-?J" #=(W""<"-?JG-?JG.HI" #=(?""<"-?JG-?JG.HI" #=(`,"<".-.G-?JGR." #=(Bg"<"-HHG-HHG-HH"

haicajb&+0#&#)/)(*3#),;"

CONVENTIONAL HUMAN CHROMOSOME COLORS 10

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 47

All chromosomes in the mouse genome. The figure uses the human karyotype file which defines 21 chromosomes (1..19, X, Y) and the cytogenetic bands.!

C67(8)084+"<"33&$707&67(8)084+3=:17,30K0" 67(8)084+"<"33&$707&67(8)084+31):*+30K0" C67(8)084+"<"" ""33&$707&67(8)084+3=:17,>1):*+30K0" C67(8)084+"<"" ""33&$707&67(8)084+3=:17,>1):*+>/7@+/*30K0"

*+**'),*&-&.?&+0#&#'(#)*3#),;"

DRAWING THE MOUSE GENOME 10

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 48

Ideograms of all human (labeled hN) and mouse (labeled mN)

• chromosomes. !

Human ideograms are shaded by the UCSC genome browser color convention.!

C67(8)084+"<"33&$707&67(8)084+3=:17,30K0" C67(8)084+"<"33&$707&67(8)084+31):*+30K0" C67(8)084+"<"" ""33&$707&67(8)084+3=:17,>1):*+30K0" 67(8)084+"<"" ""33&$707&67(8)084+3=:17,>1):*+>/7@+/*30K0"

*+**)',*&-&.?&+0#&#'(#)*3#),;"

DRAWING MULTIPLE GENOMES 10

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 49

LESSON 11

PROGRESSION & ORIENTATION

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 50

Chromosomes 1,2 of human and mouse genomes.! The ideograms start the top of the figure and progress clockwise. ! The scale of each ideogram is oriented clockwise.!

67(8)084+"<"" ""33&$707&67(8)084+3=:17,>1):*+>/7@+/*30K0" #=()1)*)1+*>$'*4/78>$+;7:/0"<",)" #=()1)*)1+*"""""""<"=*.S=*-S11.S11-" #=()1)*)1+*>)($+("<"=*.S=*-S11-S11."

*+**'),*&-&..&+0#&#'(#)*3#),;"

IDEOGRAM SELECTION 11

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 51

Scale on mouse ideograms is oriented counter-clockwise,

• pposite to the scale on the human ideograms. This makes

adjacent the start and end of chromosomes 1 and 2 from the two species.!

#=()1)*)1+*>(+N+(*+"<"11-S11."

*+**'),*&-&..&+0#&#'(#)*3#),;"

SCALE REVERSAL 11

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 52

Scale of each ideogram has been adjusted so that it occupies " of the figure.!

#=()1)*)1+*>*#7/+"""<" =*-X.3?.OS11.X.3-HJS11-X.3IR?"

*+**'),*&-&..&+0#&#'(#)*3#),;"

FITTING IDEOGRAMS TO 25% OF FIGURE 11

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 53

LESSON 12

RELATIVE & ABSOLUTE TICKS

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 54

Ticks have been added inside (relative ticks) and outside (absolute ticks) the ideogram circle.!

*=)D>0'#6*""""""""""<"8+*" *=)D>0'#6>/7@+/*""""<"8+*" 90'#6*!" (7$':*""""""""""<"" ""$'1*E'$+)5(71G(7$':*>):0+(F"k"JH4" C"7@*)/:0+"0'#6*"E*47#',5"'*"" C"$+;',+$"@8"47(71+0+("]*47#',5^F" 90'#6!" *47#',5""""""""<"-?:" *'V+"""""""""""<".-4" 0='#6,+**""""""<"-4" *=)D>/7@+/"""""<"8+*" /7@+/>*'V+"""""<".?4" ;)(170"""""""""<"Y$" 9&0'#6!"

*+**'),*&-&.-&+0#&0'#6*3#),;"

ABSOLUTE TICKS – 20 MB SPACING 12

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 55

Chromosomes 1,2 of human and mouse genomes, with adjusted format parameters to make the ideograms thinner, shrink the ideogram circle and remove ideogram color.!

90'#6!" *47#',5""""""""<".?:" *'V+"""""""""""<"P4" 0='#6,+**""""""<"-4" *=)D>/7@+/"""""<",)" 9&0'#6!" 90'#6!" *47#',5""""""""<"-:" *'V+"""""""""""<"I4" 0='#6,+**""""""<"-4" *=)D>/7@+/"""""<",)" 9&0'#6!"

*+**'),*&-&.-&+0#&0'#6*3#),;"

ABSOLUTE TICKS – 10 AND 2 MB SPACING 12

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 56

Chromosomes 1,2 of human and mouse genomes, with adjusted format parameters to make the ideograms thinner, shrink the ideogram circle and remove ideogram color.!

90'#6!" (7$':*"""""""""<"?3PH(" /'"01234&$'()))*)#(5"&16() #/'"0123)))))))*)7+78) *'V+"""""""""""<"I4" 0='#6,+**""""""<".4" *=)D>/7@+/"""""<",)" 9&0'#6!" 90'#6!" (7$':*"""""""""<"?3PH(" /'"01234&$'()))*)#(5"&16() #/'"0123)))))))*)7+97) *'V+"""""""""""<"R4" 0='#6,+**""""""<".4" *=)D>/7@+/"""""<"8+*" /7@+/>(+/70'N+"<"8+*" (1:/0'4/'+(""""<".??" ;)(170"""""""""<"Y$" /:;;1.)))))))))*)<) 9&0'#6!"

*+**'),*&-&.-&+0#&0'#6*3#),;"

RELATIVE TICKS – 10 AND 2 % SPACING 12

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 57

/=%>43#1-)))))))*)$(/) 90'#6!" *47#',5""""""""<"-?:" *'V+"""""""""""<".-4" 0='#6,+**""""""<"-4" *=)D>/7@+/"""""<"8+*" /7@+/>*'V+"""""<".?4" ;)(170"""""""""<"Y$" 3#1-4/&"#&)))))*)9#) 3#1-4(2-)))))))*)9#?@A') 3#1-40%5%#)))))*)6-3#($) 3#1-4&=10!2(//)*)9') 3#1-)))))))))))*)$(/) 9&0'#6!"

*+**'),*&-&.-&+0#&0'#6*3#),;"

GRIDS 12

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 58

Highlight regions placed immediately inside the outer tick ring provide a visual color index for the ideograms.!

9='5=/'5=0*!" 9='5=/'5=0!" ;'/+"<"33&$707&='5=/'5=030K0" (?"""<".(kJ?4" (."""<".(kJH4" 9&='5=/'5=0!" 9&='5=/'5=0*!" =*."?"-JP-JQP.Q";15540%5%#*B-8C9) =*-"?"-J-QH..JQ";15540%5%#*B-8C8) 11."?".QP.QHJI-";15540%5%#*B-8C@) 11-"?".O.PJO?OP";15540%5%#*B-8CD)

*+**'),*&-&.-&+0#&#'(#)*3#),;"

HIGHLIGHTS 12

*+**'),*&-&$707&='5=/'5=030K0"

SESSION 2 / DATA TRACKS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS Martin Krzywinski martink@bcgsc.ca 59