#install.packages('BioCircos')# You need devtools for that
if (!require('devtools')){install.packages('devtools')}## Loading required package: devtools## Loading required package: usethisdevtools::install_github('lvulliard/BioCircos.R', build_vignettes = TRUE)## Skipping install of 'BioCircos' from a github remote, the SHA1 (99db7644) has not changed since last install.
## Use `force = TRUE` to force installationTo produce a BioCircos visualization, you need to call
the BioCircos method, that accepts
a tracklist containing the different tracks to be
displayed, the genome to be displayed and plotting parameters.
By default, an empty tracklist is used, and the genome is
automatically set to use the chromosome sizes of the reference genome
hg19 (GRCh37).
library(BioCircos)
BioCircos()A genome needs to be set in order to map all the coordinates of the tracks on it.
For now, the only pre-configured genome available is hg19 (GRCh37), for which the length of the main 22 genomic autosomal chromosome pairs and of the sexual chromosomes are available. The Y chromosome can be removed using the ychr parameter. Visual parameters are also available, such as by giving a vector of colors or a RColorBrewer palette to change the colors of each chromosome (paramter genomeFillColor), the space between each chromosome (chrPad) or their borders (displayGenomeBorder).
The ticks, displaying the scale on each chromosome, can be removed with genomeicksDisplay, and the genome labels (chromosome names) can be brought closer or further away from the chromosomes with genomeLabelDy.
library(BioCircos)
BioCircos(genome = 'hg19', yChr = FALSE, genomeFillColor = "Reds", chrPad = 0, displayGenomeBorder = FALSE, genomeTicksDisplay = FALSE, genomeLabelDy = 0)To use your own reference genome, you need to define a named list of chromosomal lengths and use it as the genome parameter. The names and lengths should match the coordinates you plan on using later for your tracks.
You may want to change the scale of the ticks on the chromosomes, to fit to your reference genome, with the genomeTickScale parameters.
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)The different levels of information will be displayed on different tracks of different types and located at different radii on the visualization. All the track-generating functions of this package return tracklists that can be added together into a single tracklist, to be given as the tracks argument of the BioCircos method.
The different kinds of tracks are presented in the folloing sections.
All tracks need to be named.
A first track simply corresponds to text annotations. The obligatory parameters are the track name and the text to be displayed. Some parameters such as the size, the opacity and the coordinates can be customized.
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)To map punctual information associated with a single-dimensional value on the reference genome, such as a variant or a SNP associated with a confidence score, SNP tracks can be used.
It is therefore needed to specify the chromosome and coordinates where such points are mapped, as well as the corresponding value, which will be used to compute the radial coordinate of the points.
By default, points display a tooltip when hovered by the mouse.
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)Arc tracks are displaying arcs along the genomic circle, between the radii given as the minRadius and maxRadius parameters. As for an SNP track, the chromosome and coordinates (here corresponding to the beginning and end of each arc) should be specified.
By default, arcs display a tooltip when hovered by the mouse.
library(BioCircos)
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)Links track represent links between different genomic position. They are displayed at the center of the visualization, and out to a radius specified by the maxRadius parameter. The chromosomes and beginning and end positions of the regions to be linked are necessary, and labels can be added.
By default, links display a tooltip when hovered by the mouse.
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, labelSize = 8)
BioCircos(tracklist, genomeFillColor = "PuOr",
chrPad = 0.02, displayGenomeBorder = FALSE, yChr = FALSE,
genomeTicksDisplay = FALSE, genomeLabelTextSize = "8pt", genomeLabelDy = 0)Bar plots may be added on another type of tracks. The start and end coordinates of each bar, as well as the associated value should be specified.
By default, the radial range of the track will be stretch from the minimal to the maximum value of the track, but other boundaries may be specified with the range parameter.
Here, to add a track to the tracklist at each iteration of the loop, we initialze the tracks tracklist with an empty BioCircosTracklist object.
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) Conceptually close to bar tracks, and commonly used for purposes such
as representation of copy number variants, the CNV tracks consist of
arcs at a given radial distance showing a value associated with a genome
stretch.
The start and end coordinates of each arc, as well as the associated
value need to be specified.
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)For a given genome stretch, heatmaps associate linearly numerical
values with a color range.
For two-dimensional heatmaps, you can stack up heatmap tracks,
as done in the following example.
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")The Line tracks display segments on a track. They are
defined by the set of vertices that will be joined to produce the
segments.
If the vertices provided span multiple chromosomes, the segments between
the last point on a chromosome and the first point on the next
chromosome will be discarded.
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!")Tracks can be removed from a track list by substracting the name of the corresponding track.
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')combine and overlap as many tracks as you want.
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)The data is circos_data_clean.csv. This plot displays all variants with magnitude greater than one. Variants that are magnitude lower than 2 should be displayed in green, 2-3 in orange, and 3 or greater in red.
library(BioCircos)
# Load data from CSV file
variants_data <- read.csv("~/Desktop/OneDrive - Johns Hopkins/24spring/AAG/AAG_L6_exercises/circos_data_clean.csv")
# Filter variants with magnitude greater than one
filtered_variants <- variants_data[variants_data$Magnitude > 1, ]
# Assign colors based on magnitude
filtered_variants$Color <- ifelse(filtered_variants$Magnitude >= 3, 'red', ifelse(filtered_variants$Magnitude >= 2, 'orange', 'green'))
# Extract the necessary components for the plot
points_chromosomes <- as.character(filtered_variants$Chrom)
points_coordinates <- as.numeric(filtered_variants$Pos)
points_values <- as.numeric(filtered_variants$Magnitude)
points_colors <- as.character(filtered_variants$Color)
# Define the SNP track
tracklist <- BioCircosSNPTrack('mySNPTrack', points_chromosomes, points_coordinates, points_values, colors = points_colors, minRadius = 0.5, maxRadius = 0.9)
# Add a background track
tracklist <- tracklist + BioCircosBackgroundTrack('myBackgroundTrack', minRadius = 0.5, maxRadius = 0.9,borderColors = '#AAAAAA', borderSize = 0.6, fillColors = '#B3E6FF')
# Generate the BioCircos plot
BioCircos(tracklist, genomeFillColor = 'PuOr', chrPad = 0.05, displayGenomeBorder = FALSE, yChr = FALSE, genomeTicksDisplay = FALSE, genomeLabelTextSize = 9, genomeLabelDy = 0)