Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
2 — Quick Start
7. Heat maps
Heat maps are used for data types which associate a value with a genomic position, or region. As such, this track uses the same data format as histograms.
The track linearly maps a range of values [min,max] onto a
list of colors c[n], i=0..N.
f = (value - min) / ( max - min )
n = 0 if f < 0
N if f > 1
N * f otherwise
The track shares many of the same format parameters with a histogram. As usual, you need to define the type, file and r0/r1 parameters.
<plot> type = heatmap file = data/5/segdup.hs1234.heatmap.txt r1 = 0.89r r0 = 0.88r </plot>
linear vs power scaling
If scale_log_base is used, the mapping is not linear, but a power law
n = N * f**(1/scale_log_base)
When scale_log_base > 1 the dynamic range for values close to min is expanded. When scale_log_base < 1 the dynamic range for values close to max is expanded.
scale_log_base = 5
colors
Heat map colors are defined by a combination of CSV or color lists.
In this tutorial, the heat map color range is made up of 5 levels of transparency of chromosome colors, plus a fully opaque version of the color.
color = hs1_a5,hs1_a4,hs1_a3,hs1_a2,hs1_a1,hs1
A large number of colors and color lists are defined by default (see etc/colors.conf in the Circos distribution.
common colors
Common colors (red, green, blue, purple, orange, yellow, grey) are defined in 7 tones. Where possible, these are taken from Brewer palletes.
vvlHUE very very light HUE (e.g. vvlred) vlHUE very light lHUE light HUE dHUE dark vdHUE very dark vvdHUE very very dark
Colors white and black are also defined, as is transparent.
cytogenetic band colors
Colors for conventional cytogenetic band patterns are defined
gposNNN # NNN = 25, 33, 50, 66, 75, 100
gpos
gvar
gneg
acen
stalk
human chromosome color scheme
The UCSC browser uses a conventional color scheme for human chromosomes. These colors are defined as
chr1 chr2 ... chr22 chrx chry chrm chrun
Synonyms with hs prefix are also defined (e.g. chr1 and hs1).
Luminance corrected chromosome palettes are defined for L= 70, 80 and 90
lumLchr* # L=70,80,90 e.g. lum70chr1 lum90chr11
brewer palettes
All Brewer pallete colors are available through the syntax
PALETTE-N-TYPE-M
for color M (M=1..N) in the N-color brewer palette PALETTE of type TYPE (TYPE=seq|div|qual). For each PALETTE, there are several versions for different values of N=I..J.
I J
TYPE=seq
blues 3 9
bugn 3 9 # blue-green
bupu 3 9 # blue-purple
gnbu 3 9 # green-blue
greens 3 9
greys 3 9
oranges 3 9
orrd 3 9 # orange-red
pubu 3 9 # purple-blue
pubugn 3 9 # purple-blue-green
purd 3 9 # purple-red
purples 3 9
rdpu 3 9 # red-purple
reds 3 9
ylgn 3 9 # yellow-green
ylgnbu 3 9 # yellow-green-blue
ylorbr 3 9 # yellow-orange-brown
ylorrd 3 9 # yellow-orange-red
e.g. blues-9-seq-3 (3rd color in 9 color blues palette)
rdpu-3-seq-1 (1st color in 3 color red-purple sequential palette)
TYPE=div
brbg 3 11 # brown-blue-green
piyg 3 11 # pink-yellow-green
prgn 3 11 # purple-green
puor 3 11 # purple-orange
rdbu 3 11 # red-blue
rdgy 3 11 # red-green
rdylbu 3 11 # red-yellow-blue
rdylgn 3 11 # red-yellow-green
spectral 3 11 # rainbow: red-orange-yellow-green-blue
e.g. piyg-11-div-2 (2rd color in 11 color pink-yellow-green diverging palette)
TYPE=qual
accent 3 8
dark2 3 8
paired 3 12
pastel1 3 9
pastel2 3 8
set1 3 9
set2 3 8
set3 3 12
e.g. set1-5-qual-1 (1st color in 5 color set1 qualitative palette)
pure hues
For each pure hue H in HSV space, the color hueHHH is defined
hue000 hue001 hue002 ... hue359 hue360
Color lists
Color lists are named sets of colors used for parameters which accept a list (e.g. heat map color parameter).
Lists exist for all Brewer palettes, of the format PALETTE-N-TYPE. For example, reds-5-seq, spectral-7-div and set3-5-qual are all lists.
Pure hue lists are available, hue-sN, for each hue step of N (e.g. hue-s2, hue-s5, ...). For example, hue-s5 list is made up of the colors hue000, hue005, hue010, hue015, and so on.
N-color hue lists are available as hue-N (e.g. hue-3, hue-10, ...). For example, hue-10 is made up of the 10 colors hue000, hue036, hue072, ... hue324. It is the same list as hue-s32.
transparency
Color transparency is specified using the suffix _aN for transparency level N. The number of allowable levels is controled by the auto_alpha_steps parameter in etc/image.generic.conf. By default this is set to 5 which allows for 5 levels of transparency
green fully opaque green_a1 16% transparent green_a2 33% transparent green_a3 50% transparent green_a4 66% transparent green_a5 83% transparent