{"id":2497,"date":"2018-11-27T19:51:48","date_gmt":"2018-11-27T19:51:48","guid":{"rendered":"http:\/\/pcool.dyndns.org:8080\/statsbook\/?page_id=2497"},"modified":"2025-06-30T10:10:44","modified_gmt":"2025-06-30T09:10:44","slug":"circos-plots-biocircos","status":"publish","type":"page","link":"https:\/\/pcool.dyndns.org\/index.php\/circos-plots-biocircos\/","title":{"rendered":"Circos Plots – BioCircos"},"content":{"rendered":"\n

BioCircos1<\/a><\/sup> creates html pages. For example, without any arguments (from the examples):<\/p>\n\n\n\n

Installation of the BioCircos package should be according the the Bioconductor installation of packages<\/a>.<\/p>\n\n\n\n

The plots created with BioCircos will be rendered to html and diplayed in your browser.<\/p>\n\n\n\n

BiocManager::install('BioCircos')<\/mark><\/em>\n\nlibrary(BioCircos)<\/em><\/span>\n# https:\/\/cran.r-project.org\/web\/packages\/BioCircos\/vignettes\/BioCircos.html<\/em><\/span>\n## have a look at the multitrack example at the end!!!<\/em><\/span>\nBioCircos()<\/em><\/span><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Using hg19<\/p>\n\n\n\n
BioCircos(genome = \"hg19\", yChr = FALSE, genomeFillColor = \"Reds\", chrPad = 0, <\/span><\/em>displayGenomeBorder = FALSE, genomeTicksDisplay = FALSE, genomeLabelDy = 0)<\/span><\/em><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Custom:<\/p>\n\n\n\n
myGenome = list(\"A\" = 10560, <\/em><\/span>\"B\" = 8808,<\/em><\/span>\"C\" = 12014, <\/em><\/span>\"D\" = 7664,<\/em><\/span>\"E\" = 9403,<\/em><\/span>\"F\" = 8661)<\/em><\/span>\nBioCircos(genome = myGenome, genomeFillColor = c(\"tomato2\", \"darkblue\"), <\/em><\/span>genomeTicksScale = 4e+3)<\/em><\/span><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Text; the following code will display ‘Some text’:<\/p>\n\n\n\n
tracklist = BioCircosTextTrack('myTextTrack', 'Some text', size = \"2em\", opacity = 0.5, <\/span><\/em>x = -0.67, y = -0.5)<\/span><\/em>\nBioCircos(tracklist, genomeFillColor = \"PuOr\", <\/span><\/em>chrPad = 0, displayGenomeBorder=FALSE, <\/span><\/em>genomeTicksLen=2, genomeTicksTextSize = 0, genomeTicksScale=1e+8, <\/span><\/em>genomeLabelTextSize=\"9pt\", genomeLabelDy=0)<\/span><\/em><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Background; to change the background:<\/p>\n\n\n\n
tracklist = BioCircosBackgroundTrack(\"myBackgroundTrack\", minRadius = 0.5, maxRadius = 0.8, <\/span><\/em>borderColors = \"#AAAAAA\", borderSize = 0.6, fillColors = \"#FFBBBB\") <\/span><\/em>\nBioCircos(tracklist, genomeFillColor = \"PuOr\", <\/span><\/em>chrPad = 0.05, displayGenomeBorder = FALSE,<\/span><\/em>genomeTicksDisplay = FALSE, genomeLabelTextSize = \"9pt\", genomeLabelDy = 0)<\/span><\/em><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
SNP track:<\/p>\n\n\n\n
# Chromosomes on which the points should be displayed<\/span><\/em>\npoints_chromosomes = c('X', '2', '7', '13', '9')<\/span><\/em>\n# Coordinates on which the points should be displayed<\/span><\/em>\npoints_coordinates = c(102621, 140253678, 98567307, 28937403,20484611)<\/span><\/em>\n# Values associated with each point, used as radial coordinate<\/span><\/em>\n# on a scale going to minRadius for the lowest value to maxRadius for # the highest value<\/span><\/em>\npoints_values = 0:4<\/span><\/em>\n\ntracklist = BioCircosSNPTrack('mySNPTrack', points_chromosomes, points_coordinates,points_values, colors = c(\"tomato2\", \"darkblue\"), minRadius = 0.5, maxRadius = 0.9)<\/span><\/em>\n\n# Background are always placed below other tracks<\/span><\/em>\ntracklist = tracklist + BioCircosBackgroundTrack(\"myBackgroundTrack\",<\/span><\/em>\nminRadius = 0.5, maxRadius = 0.9, borderColors = \"#AAAAAA\", <\/span><\/em>\nborderSize = 0.6, fillColors = \"#B3E6FF\")<\/span><\/em>\n\nBioCircos(tracklist, genomeFillColor = \"PuOr\", <\/span><\/em>chrPad = 0.05, displayGenomeBorder = FALSE, yChr = FALSE, <\/span><\/em>genomeTicksDisplay = FALSE, genomeLabelTextSize = 18, genomeLabelDy = 0)<\/span><\/em><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Arc track:<\/p>\n\n\n\n
# Chromosomes on which the arcs should be displayed\narcs_chromosomes = c('X', 'X', '2', '9') \narcs_begin = c(1, 45270560, 140253678, 20484611)\narcs_end = c(155270560, 145270560, 154978472, 42512974)\n\ntracklist = BioCircosArcTrack('myArcTrack', arcs_chromosomes, arcs_begin, arcs_end, minRadius = 1.18, maxRadius = 1.25, opacities = c(0.4, 0.4, 1, 0.8))<\/mark><\/em>\nBioCircos(tracklist, genomeFillColor = \"PuOr\", <\/em><\/span>chrPad = 0.02, displayGenomeBorder = FALSE, yChr = FALSE, <\/em><\/span>genomeTicksDisplay = FALSE, genomeLabelTextSize = 0)<\/em><\/span><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Link track<\/span>:<\/p>\n\n\n\n
# Chromosomes on which the links should start<\/em><\/span>\nlinks_chromosomes_1 = c('X', '2', '9') <\/em><\/span>\n# Chromosomes on which the links should end<\/em><\/span>\nlinks_chromosomes_2 = c('3', '18', '9') <\/em><\/span>\n\nlinks_pos_1 = c(155270560, 154978472, 42512974)<\/em><\/span>\nlinks_pos_2 = c(102621477, 140253678, 20484611)<\/em><\/span>\nlinks_labels = c(\"Link 1\", \"Link 2\", \"Link 3\")<\/em><\/span>\n\ntracklist = BioCircosBackgroundTrack(\"myBackgroundTrack\", minRadius = 0, maxRadius = 0.55, borderSize = 0, fillColors = \"#EEFFEE\") <\/em><\/span>\n\ntracklist = tracklist + BioCircosLinkTrack('myLinkTrack', links_chromosomes_1, links_pos_1, links_pos_1 + 50000000, links_chromosomes_2, links_pos_2, links_pos_2 + 750000, <\/em><\/span>\nmaxRadius = 0.55, labels = links_labels)<\/em><\/span>\n\nBioCircos(tracklist, genomeFillColor = \"PuOr\", <\/em><\/span>chrPad = 0.02, displayGenomeBorder = FALSE, yChr = FALSE, <\/em><\/span>genomeTicksDisplay = FALSE, genomeLabelTextSize = \"8pt\", genomeLabelDy = 0)<\/em><\/span><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Bar track<\/span>:<\/p>\n\n\n\n
library(RColorBrewer)<\/span><\/em>\nlibrary(grDevices)<\/span><\/em>\n\n# Define a custom genome<\/span><\/em>\ngenomeChr = LETTERS<\/span><\/em>\nlengthChr = 5*1:length(genomeChr)<\/span><\/em>\nnames(lengthChr) <- genomeChr<\/span><\/em>\n\ntracks = BioCircosTracklist()<\/span><\/em>\n# Add one track for each chromosome<\/span><\/em>\nfor (i in 1:length(genomeChr)){<\/span><\/em>\n  # Define histogram\/bars to be displayed<\/span><\/em>\n  nbBars = lengthChr[i] - 1<\/span><\/em>\n  barValues = sapply(1:nbBars, function(x) 10 + nbBars%%x)<\/span><\/em>\n  barColor = colorRampPalette(brewer.pal(8, \"YlOrBr\"))(length(genomeChr))[i]<\/span><\/em>\n  # Add a track with bars on the i-th chromosome<\/span><\/em>\n  tracks = tracks + BioCircosBarTrack(paste0(\"bars\", i), chromosome = genomeChr[i], starts = (1:nbBars) - 1, ends = 1:nbBars, values = barValues, color = barColor, range = c(5,75))<\/span><\/em>\n}<\/span><\/em>\n# Add background<\/span><\/em>\ntracks = tracks + BioCircosBackgroundTrack(\"bars_background\", <\/span><\/em>\ncolors = \"#2222EE\")<\/span><\/em>\n\nBioCircos(tracks, genomeFillColor = \"YlOrBr\", genome = as.list(lengthChr), <\/span><\/em>genomeTicksDisplay = F, genomeLabelDy = 0)<\/span><\/em><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
CNV tracks<\/span>:<\/p>\n\n\n\n
# Arcs coordinates<\/span><\/em>\nsnvChr = rep(4:9, 3)<\/span><\/em>\nsnvStart = c(rep(1,6), rep(40000000,6), rep(100000000,6))<\/span><\/em>\nsnvEnd = c(rep(39999999,6), rep(99999999,6), 191154276, 180915260, 171115067, 159138663, 146364022, 141213431)<\/span><\/em>\n# Values associated with each point, used as radial coordinate <\/span><\/em>\n# on a scale going to minRadius for the lowest value to maxRadius for # the highest value<\/span><\/em>\nsnvValues = (1:18%%5)+1<\/span><\/em>\n# Create CNV track<\/span><\/em>\ntracks = BioCircosCNVTrack('cnv_track', as.character(snvChr), snvStart, snvEnd, snvValues, color = \"#CC0000\", range = c(0,6))<\/span><\/em>\n\n# Add background<\/span><\/em>\ntracks = tracks + BioCircosBackgroundTrack(\"arcs_background\", <\/span><\/em>\ncolors = \"#2222EE\")<\/span><\/em>\nBioCircos(tracks, genomeFillColor = \"YlOrBr\", genomeTicksDisplay = F, genomeLabelDy = 0)<\/span><\/em><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Heatmap tracks:<\/p>\n\n\n\n
# Define a custom genome<\/span><\/em>\ngenomeChr = LETTERS[1:10]<\/span><\/em>\nlengthChr = 5*1:length(genomeChr)<\/span><\/em>\nnames(lengthChr) <- genomeChr<\/span><\/em>\n\n# Define boxes positions<\/span><\/em>\nboxPositions = unlist(sapply(lengthChr, seq))<\/span><\/em>\nboxChromosomes = rep(genomeChr, lengthChr)<\/span><\/em>\n\n# Define values for two heatmap tracks<\/span><\/em>\nboxVal1 = boxPositions %% 13 \/ 13<\/span><\/em>\nboxVal2 = (7 + boxPositions) %% 17 \/ 17<\/span><\/em>\n\ntracks = BioCircosHeatmapTrack(\"heatmap1\", boxChromosomes, boxPositions - 1, boxPositions, boxVal1, minRadius = 0.6, <\/span><\/em>\nmaxRadius = 0.75)<\/span><\/em>\ntracks = tracks + BioCircosHeatmapTrack(\"heatmap1\", boxChromosomes, boxPositions - 1, boxPositions, boxVal2, minRadius = 0.75, <\/span><\/em>\nmaxRadius = 0.9, color = c(\"#FFAAAA\", \"#000000\"))<\/span><\/em>\n\nBioCircos(tracks, genome = as.list(lengthChr), genomeTicksDisplay = F, genomeLabelDy = 0, <\/span><\/em>HEATMAPMouseOverColor = \"#F3C73A\")<\/span><\/em><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Line tracks:<\/p>\n\n\n\n
chrVert = rep(c(1, 3, 5), c(20,10,5))<\/span><\/em>\nposVert = c(249250621*log(c(20:1, 10:1, 5:1), base = 20))<\/span><\/em>\n\ntracks = BioCircosLineTrack('LineTrack', as.character(chrVert), posVert, values = cos(posVert))<\/span><\/em>\ntracks = tracks + BioCircosLineTrack('LineTrack2', as.character(chrVert+1), 0.95*posVert, values = sin(posVert), <\/span><\/em>\ncolor = \"#40D4B9\")<\/span><\/em>\ntracks = tracks + BioCircosBackgroundTrack('Bg', <\/span><\/em>\nfillColors = '#FFEEBB', borderSize = 0)<\/span><\/em>\n\nBioCircos(tracks, chrPad = 0.05, displayGenomeBorder = FALSE, LINEMouseOutDisplay = FALSE, <\/span><\/em>\nLINEMouseOverTooltipsHtml01 = \"Pretty lines<br\/>COOL!\")<\/span><\/em>\n<\/code><\/pre>\n\n\n\n
When you hover with the mouse over the track, it will display: ‘Pretty lines COOL!<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
Multi-track example<\/span>:<\/p>\n\n\n\n
# Fix random generation for reproducibility<\/span><\/em>\nset.seed(3)<\/span><\/em>\n\n# SNP tracks<\/span><\/em>\ntracks = BioCircosSNPTrack(\"testSNP1\", as.character(rep(1:10,10)), round(runif(100, 1, 135534747)), runif(100, 0, 10), <\/span><\/em>\ncolors = \"Spectral\", minRadius = 0.3, maxRadius = 0.45)<\/span><\/em>\ntracks = tracks + BioCircosSNPTrack(\"testSNP2\", <\/span><\/em>\n  as.character(rep(1:15,5)), round(runif(75, 1, 102531392)), <\/span><\/em>\nrunif(75, 2, 12), colors = c(\"#FF0000\", \"#DD1111\", \"#BB2222\", \"#993333\"), maxRadius = 0.8, range = c(2,12))<\/span><\/em>\n# Overlap point of interest on previous track, fix range to use a <\/span><\/em>\n#<\/mark><\/em> similar scale<\/span><\/em>\ntracks = tracks + BioCircosSNPTrack(\"testSNP3\", \"7\", 1, 9, <\/span><\/em>\n  maxRadius = 0.8, size = 6, range = c(2,12))<\/span><\/em>\n\n# Background and text tracks<\/span><\/em>\ntracks = tracks + BioCircosBackgroundTrack(\"testBGtrack1\", minRadius = 0.3, maxRadius = 0.45, borderColors = \"#FFFFFF\", borderSize = 0.6) <\/span><\/em>\ntracks = tracks + BioCircosBackgroundTrack(\"testBGtrack2\", borderColors = \"#FFFFFF\", fillColor = \"#FFEEEE\", borderSize = 0.6, maxRadius = 0.8)<\/span><\/em>\ntracks = tracks + BioCircosTextTrack(\"testText\", 'BioCircos!', <\/span><\/em>\nweight = \"lighter\", x = - 0.17, y = - 0.87)<\/span><\/em>\n\n# Arc track<\/span><\/em>\narcsEnds = round(runif(7, 50000001, 133851895))<\/span><\/em>\narcsLengths = round(runif(7, 1, 50000000))<\/span><\/em>\ntracks = tracks + BioCircosArcTrack(\"fredTestArc\", as.character(sample(1:12, 7, replace=T)),  starts = arcsEnds - arcsLengths, ends = arcsEnds, labels = 1:7, maxRadius = 0.97, minRadius = 0.83)<\/span><\/em>\n\n# Link tracks<\/span><\/em>\nlinkPos1 = round(runif(5, 1, 50000000))<\/span><\/em>\nlinkPos2 = round(runif(5, 1, 50000000))<\/span><\/em>\nchr1 = sample(1:22, 5, replace = T)<\/span><\/em>\nchr2 = sample(1:22, 5, replace = T)<\/span><\/em>\nlinkPos3 = round(runif(5, 1, 50000000))<\/span><\/em>\nlinkPos4 = round(runif(5, 1, 50000000))<\/span><\/em>\nchr3 = sample(1:22, 5, replace = T)<\/span><\/em>\nchr4 = sample(1:22, 5, replace = T)<\/span><\/em>\ntracks = tracks + BioCircosLinkTrack(\"testLink\", gene1Chromosomes = chr1, gene1Starts = linkPos1, gene1Ends = linkPos1+1, gene2Chromosomes = chr2, axisPadding = 6, color = \"#EEEE55\", width = \"0.3em\", <\/span><\/em>\nlabels = paste(chr1, chr2, sep = \"*\"), displayLabel = F, <\/span><\/em>\ngene2Starts = linkPos2, gene2Ends = linkPos2+1, maxRadius = 0.42)<\/span><\/em>\ntracks = tracks + BioCircosLinkTrack(\"testLink2\", <\/span><\/em>\ngene1Chromosomes = chr3, gene1Starts = linkPos3, <\/span><\/em>\ngene1Ends = linkPos3+5000000, axisPadding = 6, displayLabel = F,<\/span><\/em>\ncolor = \"#FF6666\", labels = paste(chr3, chr4, sep = \"-\"), gene2Chromosomes = chr4, gene2Starts = linkPos4, <\/span><\/em>\ngene2Ends = linkPos4+2500000, maxRadius = 0.42)<\/span><\/em>\n\n# Display the BioCircos visualization<\/span><\/em>\nBioCircos(tracks, genomeFillColor = \"Spectral\", yChr = T, chrPad = 0, displayGenomeBorder = F, genomeTicksLen = 3, genomeTicksTextSize = 0, genomeTicksScale = 50000000, genomeLabelTextSize = 18, <\/span><\/em>\ngenomeLabelDy = 0)<\/span><\/em><\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n","protected":false},"excerpt":{"rendered":"
BioCircos creates html pages. For example, without any arguments (from the examples): Installation of the BioCircos package should be according the the Bioconductor installation of packages. The plots created with BioCircos will be rendered to html and diplayed in your browser. Using hg19 Custom: Text; the following code will display ‘Some text’: Background; to change […]<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-2497","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/pcool.dyndns.org\/index.php\/wp-json\/wp\/v2\/pages\/2497","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pcool.dyndns.org\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pcool.dyndns.org\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pcool.dyndns.org\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/pcool.dyndns.org\/index.php\/wp-json\/wp\/v2\/comments?post=2497"}],"version-history":[{"count":2,"href":"https:\/\/pcool.dyndns.org\/index.php\/wp-json\/wp\/v2\/pages\/2497\/revisions"}],"predecessor-version":[{"id":4589,"href":"https:\/\/pcool.dyndns.org\/index.php\/wp-json\/wp\/v2\/pages\/2497\/revisions\/4589"}],"wp:attachment":[{"href":"https:\/\/pcool.dyndns.org\/index.php\/wp-json\/wp\/v2\/media?parent=2497"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}