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.
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
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
<plot> type = heatmap file = data/5/segdup.hs1234.heatmap.txt r1 = 0.89r r0 = 0.88r </plot>
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
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 (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
black are also defined, as is
Colors for conventional cytogenetic band patterns are defined
gposNNN # NNN = 25, 33, 50, 66, 75, 100 gpos gvar gneg acen stalk
The UCSC browser uses a conventional color scheme for human chromosomes. These colors are defined as
chr1 chr2 ... chr22 chrx chry chrm chrun
hs prefix are also defined (e.g.
Luminance corrected chromosome palettes are defined for L= 70, 80 and 90
lumLchr* # L=70,80,90 e.g. lum70chr1 lum90chr11
All Brewer pallete colors are available through the syntax
for color M (M=1..N) in the N-color brewer palette
PALETTE of type
TYPE=seq|div|qual). For each
PALETTE, there are several versions for different values of
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)
For each pure hue H in HSV space, the color hueHHH is defined
hue000 hue001 hue002 ... hue359 hue360
Color lists are named sets of colors used for parameters which accept a list (e.g. heat map
Lists exist for all Brewer palettes, of the format
PALETTE-N-TYPE. For example,
set3-5-qual are all lists.
Pure hue lists are available,
hue-sN, for each hue step of N (e.g.
hue-s5, ...). For example,
hue-s5 list is made up of the colors
hue015, and so on.
N-color hue lists are available as
hue-10, ...). For example,
hue-10 is made up of the 10 colors
hue324. It is the same list as
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