drawing data one genome, four samples SESSION 2 MARTIN KRZYWINSKI - PowerPoint PPT Presentation

drawing data— one genome, four samples SESSION 2 MARTIN KRZYWINSKI Genome Sciences Center BC Cancer Agency Vancouver, Canada EMBO GLOBAL EXCHANGE LECTURE COURSE: HIGH-THROUGHPUT NEXT GENERATION SEQUENCING APPLIED TO INFECTIOUS DISEASES Institut Pasteur de Tunis, Tunis, Tunesia Sep 15–25, 2014 GENOME VISUALIZATION WITH CIRCOS v20140922

SESSION FINAL IMAGE 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. 2 GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

highlights LESSON 1 GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

GENE ANNOTATION INPUT FILE > cat ../../../data/lm.gene.txt LmxM.07 425833 429915 LmxM.07.0880 type=gene,strand=+,ID=LmxM. 07.0880,Name=LmxM.07.0880,description=protein+kinase%2C +putative,size=4083,web_id=LmxM.07.0880,locus_tag=LmxM. 07.0880,size=4083,Alias=322488462,401415487,LmxM07.0880,LmxM. 07.0880,LmxM07.0880.1,LmxM07.0880.1:pep LmxM.07 441328 442218 LmxM.07.0900 type=gene,strand=+,ID=LmxM. 07.0900,Name=LmxM.07.0900,description=serine%2Fthreonine+kinase%2C +putative%2Cprotein+kinase%2C+putative,size=891,web_id=LmxM. 07.0900,locus_tag=LmxM. 07.0900,size=891,Alias=322488464,401415491,LmxM07.0900,LmxM. 07.0900,LmxM07.0900.1,LmxM07.0900.1:pep GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

GENES AS HIGHLIGHTS # 2/1/etc/circos.conf chromosomes_units = 1000 chromosomes = -/00/ chromosomes_color = /./=white <plots> <plot> type = highlight file = conf(datadir)/lm.gene.txt fill_color = black r1 = dims(ideogram,radius_outer) r0 = dims(ideogram,radius_inner) minsize = 5u stroke_thickness = undef </plot> </plots> . GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

TRANSPARENCY # 2/1/etc/circos.conf chromosomes_units = 1000 chromosomes = -/00/ chromosomes_color = /./=white <plots> <plot> type = highlight file = conf(datadir)/lm.gene.txt fill_color = black_a4 r1 = dims(ideogram,radius_outer) r0 = dims(ideogram,radius_inner) minsize = 5u stroke_thickness = undef </plot> </plots> . GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

RULES TO SHOW PUTATIVE PROTEINS # 2/1/etc/circos.conf chromosomes_units = 1000 chromosomes = -/00/ chromosomes_color = /./=white <plots> <plot> type = highlight file = conf(datadir)/lm.gene.txt fill_color = black_a4 r1 = dims(ideogram,radius_outer) r0 = dims(ideogram,radius_inner) minsize = 5u stroke_thickness = undef <rules> <rule> condition = var(description) =~ /putative/ fill_color = red z = 5 </rule> </rules> </plot> </plots> . GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

heatmaps LESSON 2 GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

HEATMAPS, 4 SAMPLES # 2/2/etc/circos.conf <plot> type = heatmap r1 = 0.80r r0 = 0.76r file = conf(datadir)/lm.exp.ah063.txt color = reds-8-seq scale_log_base = 0.5 minsize = 25u <<include rules.heatmap.conf>> </plot> <plot> type = heatmap r1 = 0.75r r0 = 0.71r file = conf(datadir)/lm.exp.ah064.txt color = reds-8-seq scale_log_base = 0.5 minsize = 25u <<include rules.heatmap.conf>> </plot> ... . GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

HISTOGRAM # etc/rules.heatmap.conf <rules> <rule> use = yes condition = var(value) < 1000 show = no </rule> <rule> condition = 1 z = eval(var(value)) </rule> </rules> . GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

IMPORTING COMMON TRACK SETTINGS # etc/heatmap.conf The heatmap blocks had many common parameters type = heatmap <plot> file = conf(datadir)/lm.exp.ah063.txt type = heatmap color = reds-8-seq r1 = 0.80r scale_log_base = 0.5 r0 = 0.76r minsize = 25u file = <<include rules.heatmap.conf>> conf(datadir)/lm.exp.ah063.txt color = reds-8-seq scale_log_base = 0.5 minsize = 25u # 2/2/etc/circos.conf <<include rules.heatmap.conf>> </plot> <plot> <<include heatmap.conf>> <plot> r1 = 0.80r type = heatmap r0 = 0.76r r1 = 0.75r </plot> r0 = 0.71r file = <plot> conf(datadir)/lm.exp.ah064.txt <<include heatmap.conf>> color = reds-8-seq r1 = 0.75r scale_log_base = 0.5 r0 = 0.71r minsize = 25u </plot> <<include rules.heatmap.conf>> </plot> ... 11 GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

floating histograms LESSON 3 GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

IMPORTING COMMON TRACK SETTINGS LmxM.01 14846 16843 LmxM.01.0050 exp_ah063=64,exp_ah064=195,exp_ah065=154,exp_ah066=240, exp_min=64,exp_max=240,exp_avg=163.25,exp_range=176,exp_minah=ah063,exp_maxah=ah066 LmxM.01 27727 28314 LmxM.01.0110 exp_ah063=72,exp_ah064=117,exp_ah065=127,exp_ah066=212, exp_min=72,exp_max=212,exp_avg=132,exp_range=140,exp_minah=ah063,exp_maxah=ah066 The value of each data point is the gene name, e.g. LmxM.01.0050. We can change the value by using a rule <rule> condition = 1 value = eval(var(exp_ah063)) </rule> 13 GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

ABSOLUTE IDEOGRAM SCALE # 2/3/etc/circos.conf <plot> sample = ah063 r1 = 0.78r r0 = 0.74r <<include heatmap.conf>> </plot> ... # etc/heatmap.conf type = heatmap color = reds-8-seq scale_log_base = 0.5 minsize = 25u <<include rules.heatmap.conf>> # etc/rules.heatmap.conf <rules> <rule> condition = 1 value = eval(var(exp_conf(.,sample))) flow = continue </rule> <rule> condition = var(value) < 1000 show = no </rule> <rule> condition = 1 z = eval(var(value)) </rule> . </rules> GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

FLOATING HISTOGRAM # 2/3/etc/circos.conf <plot> type = histogram float = yes r0 = 0.80r r1 = 0.90r fill_color = black stroke_thickness = undef min = 0 max = 300 minsize = 20u <<include etc/axes.conf>> <rules> <rule> condition = 1 value = eval(sqrt(var(exp_max))) valuebase = eval(sqrt(var(exp_min))) #flow = continue </rule> <rule> condition = var(exp_range) < 1000 fill_color = grey z = -10 </rule> <rule> condition = var(exp_range) > 10000 fill_color = red z = 10 </rule> </rules> </plot> . </plots> GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

FLOATING HISTOGRAM # 2/3/etc/circos.conf <backgrounds> use = yes <background> y1 = 50 color = vvlgrey </background> <background> y0 = 150 color = vvlred </background> </backgrounds> . GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

FLOATING HISTOGRAM # 2/3/etc/circos.conf <rules> <rule> condition = 1 value = eval(sqrt(var(exp_max))) valuebase = eval(sqrt(var(exp_min))) flow = continue </rule> <rule> condition = var(exp_range) < 1000 fill_color = grey z = -10 </rule> <rule> condition = var(exp_range) > 10000 fill_color = red z = 10 </rule> </rules> . GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

scatter plot LESSON 4 GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples

IMPORTING COMMON TRACK SETTINGS LmxM.01 14846 16843 LmxM.01.0050 exp_ah063=64,exp_ah064=195,exp_ah065=154,exp_ah066=240, exp_min=64,exp_max=240,exp_avg=163.25,exp_range=176,exp_minah=ah063,exp_maxah=ah066 The value of each data point is the gene name, e.g. LmxM.01.0050. We can use the name of the sample at which expression was minimum to draw/hide a point <rule> condition = var(exp_minah) ne “ah063” show = no </rule> As before, we can change the value by using a rule <rule> condition = 1 value = eval(var(exp_ah063)) </rule> 19 GENOME VISUALIZATION WITH CIRCOS · Session 2 · Drawing data—one genome, four samples