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

SESSION 2 / DATA TRACKS SESSION 2 IDEOGRAM LAYOUT GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 1 Martin Krzywinski martink@bcgsc.ca

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

SESSION 2 / DATA TRACKS FINAL FIGURE 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. GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 3 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS LESSON 1 DRAWING IDEOGRAMS GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 4 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 SWITCH TO SESSION 2 LESSON 1 DIRECTORY !"#$"%&#'(#)*&*+**'),*&-&." !"/*" +0# "1'*# "*-2.34,5" GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 5 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 CONFIGURATION FILE *+**'),*&-&+0#&#'(#)*3#),;" The 67(8)084+ parameter is used to 99',#/:$+"'$+)5(713#),;!!"" specify the file that defines the 99',#/:$+"0'#6*3#),;!!" chromosome number and size for the genome (or genomes) to be drawn. 9'175+!" ;'/+"<"*-2.34,5" 99',#/:$+"33&+0#&'175+3#),;!!" 9&'175+!" !"#$%&$'()*)++,-"&",!"#$%&$'(+&.& " #=()1)*)1+*>:,'0*"""""""""""<".??????" #=()1)*)1+*>$'*4/78>$+;7:/0"<"8+*" 99',#/:$+"33&33&+0#&=):*+6++4',53#),;!!" GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 6 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 KARYOTYPE FILE *+**'),*&-&$707&67(8)084+30K0" The last field is the color. C";'(*0"0D)";'+/$*"E#=("2F"7(+"(+A:'(+$G";)//)D+$"@8" Color names @AB2, correspond to a C"#=()1)*)1+",71+"E#=(-F" Brewer palette. 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" GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 7 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 BREWER PALETTES *+**'),*&+0#&@(+D+(3#),;" 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" A 5-color qualitative Brewer palette. For other schemes, see www.colorbrewer.org ! GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 8 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 FIXED ABSOLUTE SPACING *+**'),*&-&.&+0#&'$+)5(713#),;" 9'$+)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'*+!" Five ideograms, arranged clockwise from 12 o’clock. ! GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 9 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 FIXED ABSOLUTE SPACING !"#$"%&#'(#)*&*+**'),*&-&." !"(:,#'(#)*" 333" #(+70+$"'175+"70"3&*-2.34,5" Five ideograms, arranged clockwise from 12 o’clock. ! GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 10 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 INCREASING SPACING *+**'),*&-&.&+0#&'$+)5(713#),;" 9'$+)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'*+!" Changing the spacing from 2u to 10u has increased spacing by 5- fold. ! GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 11 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 CHANGING SPACING BETWEEN PAIRS *+**'),*&-&.&+0#&'$+)5(713#),;" 9'$+)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'*+!" Spacing between individual ideogram pairs can be adjusted independently. This is done using the 947'(D'*+!" block. ! GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 12 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 1 CHANGING SPACING BETWEEN PAIRS *+**'),*&-&.&+0#&'$+)5(713#),;" 9'$+)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'*+!" 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. ! GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 13 Martin Krzywinski martink@bcgsc.ca

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

SESSION 2 / DATA TRACKS 1 SWITCH TO SESSION 2 LESSON 2 DIRECTORY !"#$"%&#'(#)*&*+**'),*&-&-" !"/*" +0# "*-2-34,5" GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 15 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 2 RELATIVE SPACING *+**'),*&-&-&+0#&'$+)5(713#),;" 9'$+)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.(" 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. ! GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 16 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS 2 ABSOLUTE AND RELATIVE SPACING *+**'),*&-&-&+0#&'$+)5(713#),;" 9'$+)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'*+!" Absolute and relative spacing can be used in the same figure. 9&*47#',5!" Here, default ideogram spacing is relative ( 0.1r ), but spacing between the first four chromosomes is set to 0u , 1u and 2u , respectively. ! GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 17 Martin Krzywinski martink@bcgsc.ca

SESSION 2 / DATA TRACKS LESSON 3 IDEOGRAM SCALE GENOME VISUALIZATION WITH CIRCOS DATA TRACKS 18 Martin Krzywinski martink@bcgsc.ca