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.
Stacked histograms are an extenstion of the histogram track. To plot stacked histograms, the only adjustment you require is to provide a series of values for each histogram bin in your data file.
For example, here is a part of a data file for a stacked histogram in which 5 data sets are stacked.
... hs7 65000000 69999999 0.388090,0.070074,0.547485,0.842239,0.525658 hs7 70000000 74999999 0.886542,0.321023,0.145677,0.897684,0.264217 hs7 75000000 79999999 0.854199,0.567889,0.574767,0.656331,0.418385 hs7 80000000 84999999 0.286509,0.201049,0.552485,0.876529,0.999801 hs7 85000000 89999999 0.154836,0.515471,0.389453,0.440168,0.475127 ...
The first value will appear at the bottom of the bin's stack, then the second, then third, and so on.
Individual format parameters (color
, thickness
fill_color
, pattern
) for each data sets can be specified by providing a list of comma-separated values.
For example, to make each data set filled with a different color, provide five different values for fill_color
.
fill_color = red,orange,yellow,green,blue
If you provide parameter values than data sets, they will be cycled.
Assigning individual values for color and thickness can produce useful displays, particularly when color=white
and thickness
is varied.
color = white fill_color = red,orange,yellow,green,blue fill_under = yes thickness = 1,2,3,4,5
You can independently cycle bins' color and pattern.
fill_color = red,grey,black pattern = checker,solid
will create the following bins
color pattern red checker grey solid black checker red solid grey checker black solid ... ...
By default, the bins are stacked in order of appearance of their values in the data file. Thus, given the colors
fill_color = red,orange,yellow,green,blue
the data line
hs1 0 4999999 0.237788,0.291066,0.845814,0.152208,0.585537
the bins will stack in the following order
However, when
sort_bin_values = yes
is used, the bins will be stacked by decreasing value