LINKS AND RULES GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 1 - PowerPoint PPT Presentation

SESSION 4 / LINKS AND RULES SESSION 4 LINKS AND RULES GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 1 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES LESSON PLAN ideogram, tick, grid and label layout drawing links rules – coloring links by position, part 1 rules – coloring links by position, part 2 bundling links density histograms scatter plots rules – coloring links by size GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 2 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES LINKS Examples of how rules and links are combined. (A) Original data set. (B) Color of certain links is modified using rules. (C) Geometry of nearby intra-chromosomal links has been adjusted to point the link outwards. (D) Rules were used to change the thickness of links. GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 3 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES LINKS AS BUNDLES Links are defined by two regions, which can be of any size. top By default, links are drawn as lines (with adjustable, but constant, thickness). The lines start and end in the middle of the regions that define the link. bottom When the regions that define the link are large, it is helpful to use the thickness of the link to reflect the region size. To do this, links can be drawn as ribbons whose ends take on the thickness GENOME VISUALIZATION WITH CIRCOS of the regions that define the link. When links are drawn as ribbons, LINKS AND RULES 4 thickness is not necessarily constant across the link. Depending on the Martin Krzywinski martink@bcgsc.ca orientation of the start and end regions, and the relative orientation of

SESSION 4 / LINKS AND RULES LESSON 1 IDEOGRAM, TICK, GRID AND LABEL LAYOUT GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 5 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 1 4(44"#4:6:8:(2$:$",$*4/$*#0) !!"#$%&'()"'(*+,-./$*#011) !!"#$%&'()2"$34/$*#011) !".-+(1) 0"%()5)4678/9#+) !!"#$%&'()//://:(2$:".-+(/$*#011) !:".-+(1) 3-,;*2;9()5)//:'-2-:3-,;*2;9(/<&.-#=.*&4(=%->(%4/2?2) $<,*.*4*.(4=&#"24)))))))))))5)8@@@@@@) $<,*.*4*.(4='"49%-;='(0-&%2)5)#*) $<,*.*4*.(4)))))))))5) ..8A..BA..CA..6A..DA..EA..FA..GA..HA..8@A) ..88A..8BA..8CA..86A..8DA..8EA..8FA..8GA..8HA<48) $<,*.*4*.(4=,(I(,4()5) ..8A..BA..CA..6A..DA..EA..FA..GA..HA..8@A) ..88A..8BA..8CA..86A..8DA..8EA..8FA..8GA..8H) $<,*.*4*.(4=>,(-34))5)7<48J8B@786@) K$<,*.*4*.(4=4$-%()))5)<48J88/G) The figure template showing mouse chromosomes 1-19 and !<"+<%"+<241) human chromosome 1. ! !<"+<%"+<21) 4<*L)5);(4) We will be rescaling the human chromosome so that it occupies 0"%()5)//:'-2-:<"+<%"+<2/2?2) " of the figure in order to reveal detail. ! ,@)))5)@/HH,) ,8)))5)@/HHH,) GENOME VISUALIZATION WITH CIRCOS !:<"+<%"+<21) LINKS AND RULES 6 Martin Krzywinski martink@bcgsc.ca !:<"+<%"+<241)

SESSION 4 / LINKS AND RULES 1 SESSION TEMPLATE IMAGE chromosomes_scale = hs1:11.8 Mouse chromosomes 1-19 occupy ! of the figure and human chromosome 1 is shown in the other ! . The human chromosome has an axis break at 120-140Mb to remove the centromere from the display (there is no data for this region). Notice that the scale of mouse chromosomes runs counter-clockwise. GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 7 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES LESSON 2 LINKS GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 8 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 2 4(44"*#4:6:B:(2$:$",$*4/$*#0) !%"#341) !%"#3)$<-"#1) 0"%())))))))))5)//:'-2-:%"#34/2?2) >(M"(,=,-'"&4)5)@,) ,-'"&4))))))))5)@/GD,) 2<"$3#(44)))))5)89) $*%*,)))))))))5)>%-$3=-D) !:%"#31) !:%"#341) The links show 2,300 top alignments between human chromosome 1 and mouse chromosomes 1-19. ! When transparency is used for link lines, it is possible to discern regions where the links are denser. The color for each link line here is black_a5. ! Compare this figure with Figure 6, where transparency was not GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES used. ! 9 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 2 BENEFIT OF TRANSPARENCY FOR LINKS When transparency is not used for link lines, dense links form a solid shape making it impossible to discern regions where the links are denser. The color for each link line here is black (note, no _aN suffix). GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 10 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES LESSON 3 RULES – COLORING LINKS BY POSITION, PART 1 GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 11 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 3 COLORING LINKS BY POSITION 4(44"#4:6:C:(2$:$",$*4/$*#0) !,&%(1) $*#'"2"*#)))5)=NOPB=)(Q)R..88R) $*%*,)))))))5)$<,88=-C) M)))))))))))5)8@) 2<"$3#(44)))5)B9) !:,&%(1) 4(44"#4:6:%"#34/2?2) ///) %"#3BB6E)<48)CHDBE6)6BE88B)) %"#3BB6E)..8)8GDEE88G)8GDHB@FF)) ///) Rules are used to color all links that impinge on mouse chromosome 11. ! GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 12 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 3 MULTIPLE COLORING LINKS 4(44"*#4:6:C:(2$:$",$*4/$*#0) !,&%(1) ".9*,2-#$())5)8@@) $*#'"2"*#)))5)=NOPB=)(Q)R..88R) $*%*,)))))))5)$<,88=-C) M)))))))))))5)8@) 2<"$3#(44)))5)B9) K)%"#34)2<-2)9-44)-,()2(42(')>;),(.-"#"#+) ,&%(4) 0%*L))))))))5)$*#2"#&() !:,&%(1) !,&%(1) ".9*,2-#$())5)H@) $*#'"2"*#)))5)=NSTSP=)(Q)R$<,88=-CR)UU) =VWXPW8=)1)B@(E)UU)=YZ[8=)!)D@(E) $*%*,)))))))5),('=-C) M)))))))))))5)B@) 2<"$3#(44)))5)C9) A second rule is added to uniquely color all mm11 links that start !:,&%(1) at 20-50Mb of hs1. ! GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 13 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES LESSON 4 RULES – COLORING LINKS BY POSITION, PART 2 GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 14 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 4 COLORING BY CHROMOSOME AND POSITION 4(44"*#4:6:6:(2$:$",$*4/$*#0) !,&%(41) !,&%(1) $*#'"2"*#)))5)=VWXPW8=)1)8@(E)UU)=YZ[8=)!) B@(E) $*%*,)))))))5)) ))(I-%\)R$<,])) ))))))))/) ))))))))4&>42,\=NOPB=^,"#'(?\=NOPB=^R.R_`8_)) ))))))))/) ))))))))R=-6R)_) M)))))))))))5)8@) 2<"$3#(44)))5)B9) !:,&%(1) !:,&%(41) Links within 10-20Mb on hs1 are colored by their destination chromosome. ! GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 15 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 4 4(44"*#4:6:6:(2$:$",$*4/$*#0) !,&%(1) $*#'"2"*#)))5)8) $*%*,)))))))5)) ))(I-%\)R$<,R)) ))))))))/)) ))))))))4&>42,\=NOPB=^,"#'(?\=NOPB=^R.R_`8_)) ))))))))/)R=-6R)_) KM)))))))))))5)8@) K2<"$3#(44)))5)B9) !:,&%(1) Using a rule, all links are colored by the chromosome associated with their ends. ! GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 16 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES LESSON 5 BUNDLING LINKS GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 17 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 5 PROCESS OF BUNDLING LINKS The bundlelinks tools is used to logically group adjacent links together, forming larger links. Links are bundled based on their size and distance to each other. Bundles are ideally drawn as ribbons, rather than lines, because bundle ends typically span a significant section of an ideogram. GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 18 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 5 DRAWING BUNDLES 4(44"*#4:6:D:(2$:$",$*4/$*#0) !%"#341) !%"#3)$<-"#1) ,">>*#))))))))5);(4) 0"%())))))))))5)//:'-2-:>&#'%(4/2?2) >(M"(,=,-'"&4)5)@,) ,-'"&4))))))))5)@/GD,) 2<"$3#(44)))))5)@9) $*%*,)))))))))5)>%-$3=-8@) !,&%(41) !,&%(1) $*#'"2"*#)))5)8)) $*%*,)))))))5)) ))(I-%\)R$<,R)) ))))))))/)) ))))))))4&>42,\=NOPB=^,"#'(?\=NOPB=^R.R_`8_) ))))))))/)R=-BR_) ,-'"&4B)))))5)@/HH,) The result of bundling links shown in Figure 10. ! M)))))))))))5)(I-%\=VabY8=_) Using radius2, the ends of the links are drawn closer to the !:,&%(1) mouse chromosomes. ! !:,&%(41) GENOME VISUALIZATION WITH CIRCOS !:%"#31) LINKS AND RULES 19 Martin Krzywinski martink@bcgsc.ca

SESSION 4 / LINKS AND RULES 5 VARIABLE LINK END POSITION 4(44"*#4:6:D:(2$:$",$*4/$*#0) M)5)(I-%\7=VabY8=_) By setting the z value to be inversely proportional to link size, small links are drawn on top. ! GENOME VISUALIZATION WITH CIRCOS LINKS AND RULES 20 Martin Krzywinski martink@bcgsc.ca