inst/doc/BioCircos.R

In BioCircos: Interactive Circular Visualization of Genomic Data using 'htmlwidgets' and 'BioCircos.js'

## ----eval=FALSE, screenshot.force = FALSE--------------------------------
#  install.packages('BioCircos')

## ----eval=FALSE, screenshot.force = FALSE--------------------------------
#  # You need devtools for that
#  if (!require('devtools')){install.packages('devtools')}
#  
#  devtools::install_github('lvulliard/BioCircos.R', build_vignettes = TRUE)

## ------------------------------------------------------------------------
library(BioCircos)

BioCircos()

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

BioCircos(genome = "hg19", yChr = FALSE, genomeFillColor = "Reds", chrPad = 0, 
  displayGenomeBorder = FALSE, genomeTicksDisplay = FALSE, genomeLabelDy = 0)

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

myGenome = list("A" = 10560,
        "B" = 8808,
        "C" = 12014,
        "D" = 7664,
        "E" = 9403,
        "F" = 8661)

BioCircos(genome = myGenome, genomeFillColor = c("tomato2", "darkblue"),
  genomeTicksScale = 4e+3)

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

tracklist = BioCircosTextTrack('myTextTrack', 'Some text', size = "2em", opacity = 0.5, 
  x = -0.67, y = -0.5)

BioCircos(tracklist, genomeFillColor = "PuOr",
  chrPad = 0, displayGenomeBorder = FALSE, 
  genomeTicksLen = 2, genomeTicksTextSize = 0, genomeTicksScale = 1e+8,
  genomeLabelTextSize = "9pt", genomeLabelDy = 0)

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

tracklist = BioCircosBackgroundTrack("myBackgroundTrack", minRadius = 0.5, maxRadius = 0.8,
  borderColors = "#AAAAAA", borderSize = 0.6, fillColors = "#FFBBBB")  

BioCircos(tracklist, genomeFillColor = "PuOr",
  chrPad = 0.05, displayGenomeBorder = FALSE, 
  genomeTicksDisplay = FALSE,  genomeLabelTextSize = "9pt", genomeLabelDy = 0)

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

# Chromosomes on which the points should be displayed
points_chromosomes = c('X', '2', '7', '13', '9')
# Coordinates on which the points should be displayed
points_coordinates = c(102621, 140253678, 98567307, 28937403, 20484611) 
# Values associated with each point, used as radial coordinate 
#   on a scale going to minRadius for the lowest value to maxRadius for the highest value
points_values = 0:4

tracklist = BioCircosSNPTrack('mySNPTrack', points_chromosomes, points_coordinates, 
  points_values, colors = c("tomato2", "darkblue"), minRadius = 0.5, maxRadius = 0.9)

# Background are always placed below other tracks
tracklist = tracklist + BioCircosBackgroundTrack("myBackgroundTrack", 
  minRadius = 0.5, maxRadius = 0.9,
  borderColors = "#AAAAAA", borderSize = 0.6, fillColors = "#B3E6FF")  

BioCircos(tracklist, genomeFillColor = "PuOr",
  chrPad = 0.05, displayGenomeBorder = FALSE, yChr =  FALSE,
  genomeTicksDisplay = FALSE,  genomeLabelTextSize = 18, genomeLabelDy = 0)

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

arcs_chromosomes = c('X', 'X', '2', '9') # Chromosomes on which the arcs should be displayed
arcs_begin = c(1, 45270560, 140253678, 20484611)
arcs_end = c(155270560, 145270560, 154978472, 42512974)

tracklist = BioCircosArcTrack('myArcTrack', arcs_chromosomes, arcs_begin, arcs_end,
  minRadius = 1.18, maxRadius = 1.25, opacities = c(0.4, 0.4, 1, 0.8))

BioCircos(tracklist, genomeFillColor = "PuOr",
  chrPad = 0.02, displayGenomeBorder = FALSE, yChr =  FALSE,
  genomeTicksDisplay = FALSE,  genomeLabelTextSize = 0)

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

links_chromosomes_1 = c('X', '2', '9') # Chromosomes on which the links should start
links_chromosomes_2 = c('3', '18', '9') # Chromosomes on which the links should end

links_pos_1 = c(155270560, 154978472, 42512974)
links_pos_2 = c(102621477, 140253678, 20484611)
links_labels = c("Link 1", "Link 2", "Link 3")

tracklist = BioCircosBackgroundTrack("myBackgroundTrack", minRadius = 0, maxRadius = 0.55,
  borderSize = 0, fillColors = "#EEFFEE")  

tracklist = tracklist + BioCircosLinkTrack('myLinkTrack', links_chromosomes_1, links_pos_1,
  links_pos_1 + 50000000, links_chromosomes_2, links_pos_2, links_pos_2 + 750000,
  maxRadius = 0.55, labels = links_labels)

BioCircos(tracklist, genomeFillColor = "PuOr",
  chrPad = 0.02, displayGenomeBorder = FALSE, yChr =  FALSE,
  genomeTicksDisplay = FALSE,  genomeLabelTextSize = "8pt", genomeLabelDy = 0)

## ----figBarTrack, fig.width=4, fig.height=4, fig.align = 'center', screenshot.force = FALSE----
library(BioCircos)
library(RColorBrewer)
library(grDevices)

# Define a custom genome
genomeChr = LETTERS
lengthChr = 5*1:length(genomeChr)
names(lengthChr) <- genomeChr

tracks = BioCircosTracklist()
# Add one track for each chromosome
for (i in 1:length(genomeChr)){
  # Define histogram/bars to be displayed
  nbBars = lengthChr[i] - 1
  barValues = sapply(1:nbBars, function(x) 10 + nbBars%%x)
  barColor = colorRampPalette(brewer.pal(8, "YlOrBr"))(length(genomeChr))[i]
  # Add a track with bars on the i-th chromosome
  tracks = tracks + BioCircosBarTrack(paste0("bars", i), chromosome = genomeChr[i], 
    starts = (1:nbBars) - 1, ends = 1:nbBars, values = barValues, color = barColor, 
    range = c(5,75))
}

# Add background
tracks = tracks + BioCircosBackgroundTrack("bars_background", colors = "#2222EE")

BioCircos(tracks, genomeFillColor = "YlOrBr", genome = as.list(lengthChr), 
  genomeTicksDisplay = F, genomeLabelDy = 0)

## ----figCNVTrack, screenshot.force = FALSE-------------------------------
library(BioCircos)

# Arcs coordinates
snvChr = rep(4:9, 3)
snvStart = c(rep(1,6), rep(40000000,6), rep(100000000,6))
snvEnd = c(rep(39999999,6), rep(99999999,6), 
  191154276, 180915260, 171115067, 159138663, 146364022, 141213431)
# Values associated with each point, used as radial coordinate 
#   on a scale going to minRadius for the lowest value to maxRadius for the highest value
snvValues = (1:18%%5)+1
# Create CNV track
tracks = BioCircosCNVTrack('cnv_track', as.character(snvChr), snvStart, snvEnd, snvValues, 
  color = "#CC0000", range = c(0,6))

# Add background
tracks = tracks + BioCircosBackgroundTrack("arcs_background", colors = "#2222EE")

BioCircos(tracks, genomeFillColor = "YlOrBr", genomeTicksDisplay = F, genomeLabelDy = 0)

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

# Define a custom genome
genomeChr = LETTERS[1:10]
lengthChr = 5*1:length(genomeChr)
names(lengthChr) <- genomeChr

# Define boxes positions
boxPositions = unlist(sapply(lengthChr, seq))
boxChromosomes = rep(genomeChr, lengthChr)

# Define values for two heatmap tracks
boxVal1 = boxPositions %% 13 / 13
boxVal2 = (7 + boxPositions) %% 17 / 17

tracks = BioCircosHeatmapTrack("heatmap1", boxChromosomes, boxPositions - 1, boxPositions,
  boxVal1, minRadius = 0.6, maxRadius = 0.75)
tracks = tracks + BioCircosHeatmapTrack("heatmap1", boxChromosomes, boxPositions - 1, 
  boxPositions, boxVal2, minRadius = 0.75, maxRadius = 0.9, color = c("#FFAAAA", "#000000"))

BioCircos(tracks, genome = as.list(lengthChr), genomeTicksDisplay = F, genomeLabelDy = 0, 
  HEATMAPMouseOverColor = "#F3C73A")

## ---- screenshot.force = FALSE-------------------------------------------
chrVert =  rep(c(1, 3, 5), c(20,10,5))
posVert = c(249250621*log(c(20:1, 10:1, 5:1), base = 20))

tracks = BioCircosLineTrack('LineTrack', as.character(chrVert), posVert, values = cos(posVert))
tracks = tracks + BioCircosLineTrack('LineTrack2', as.character(chrVert+1), 0.95*posVert, 
  values = sin(posVert), color = "#40D4B9")
tracks = tracks + BioCircosBackgroundTrack('Bg', fillColors = '#FFEEBB', borderSize = 0)

BioCircos(tracks, chrPad = 0.05, displayGenomeBorder = FALSE, LINEMouseOutDisplay = FALSE, 
  LINEMouseOverTooltipsHtml01 = "Pretty lines<br/>This tooltip won't go away!")

## ---- screenshot.force = FALSE-------------------------------------------
library(BioCircos)

# Create a tracklist with a text annotation and backgrounds
tracklist = BioCircosTextTrack('t1', 'hi')
tracklist = tracklist + BioCircosBackgroundTrack('b1')

# Remove the text annotation and display the result
BioCircos(tracklist - 't1')

## ----figMultiTrack, fig.width=5, fig.height=5, fig.align = 'center', screenshot.force = FALSE----
library(BioCircos)

# Fix random generation for reproducibility
set.seed(3)

# SNP tracks
tracks = BioCircosSNPTrack("testSNP1", as.character(rep(1:10,10)), 
  round(runif(100, 1, 135534747)), 
  runif(100, 0, 10), colors = "Spectral", minRadius = 0.3, maxRadius = 0.45)
tracks = tracks + BioCircosSNPTrack("testSNP2", as.character(rep(1:15,5)), 
  round(runif(75, 1, 102531392)), 
  runif(75, 2, 12), colors = c("#FF0000", "#DD1111", "#BB2222", "#993333"), 
  maxRadius = 0.8, range = c(2,12))
# Overlap point of interest on previous track, fix range to use a similar scale
tracks = tracks + BioCircosSNPTrack("testSNP3", "7", 1, 9, maxRadius = 0.8, size = 6,
  range = c(2,12))

# Background and text tracks
tracks = tracks + BioCircosBackgroundTrack("testBGtrack1", minRadius = 0.3, maxRadius = 0.45,
  borderColors = "#FFFFFF", borderSize = 0.6)    
tracks = tracks + BioCircosBackgroundTrack("testBGtrack2", borderColors = "#FFFFFF", 
  fillColor = "#FFEEEE", borderSize = 0.6, maxRadius = 0.8)
tracks = tracks + BioCircosTextTrack("testText", 'BioCircos!', weight = "lighter", 
  x = - 0.17, y = - 0.87)

# Arc track
arcsEnds = round(runif(7, 50000001, 133851895))
arcsLengths = round(runif(7, 1, 50000000))
tracks = 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)

# Link tracks
linkPos1 = round(runif(5, 1, 50000000))
linkPos2 = round(runif(5, 1, 50000000))
chr1 = sample(1:22, 5, replace = T)
chr2 = sample(1:22, 5, replace = T)
linkPos3 = round(runif(5, 1, 50000000))
linkPos4 = round(runif(5, 1, 50000000))
chr3 = sample(1:22, 5, replace = T)
chr4 = sample(1:22, 5, replace = T)
tracks = tracks + BioCircosLinkTrack("testLink", gene1Chromosomes = chr1, 
  gene1Starts = linkPos1, gene1Ends = linkPos1+1, gene2Chromosomes = chr2, axisPadding = 6,
  color = "#EEEE55", width = "0.3em", labels = paste(chr1, chr2, sep = "*"), displayLabel = F,
  gene2Starts = linkPos2, gene2Ends = linkPos2+1, maxRadius = 0.42)
tracks = tracks + BioCircosLinkTrack("testLink2", gene1Chromosomes = chr3, 
  gene1Starts = linkPos3, gene1Ends = linkPos3+5000000, axisPadding = 6, displayLabel = F,
  color = "#FF6666", labels = paste(chr3, chr4, sep = "-"), gene2Chromosomes = chr4,
  gene2Starts = linkPos4, gene2Ends = linkPos4+2500000, maxRadius = 0.42)

# Display the BioCircos visualization
BioCircos(tracks, genomeFillColor = "Spectral", yChr = T, chrPad = 0, displayGenomeBorder = F, 
  genomeTicksLen = 3, genomeTicksTextSize = 0, genomeTicksScale = 50000000,
  genomeLabelTextSize = 18, genomeLabelDy = 0)

## ----sessionINFO, screenshot.force = FALSE-------------------------------
sessionInfo()