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.
The fill of histogram bins can be changed based on the histogram bin value using a rule like the following.
# remap the histogram value from the range [-0.6,0.6] onto the index [0,5], then # use the index to select the color from the list # dorange orange lorange lblue blue dblue # # Perl syntax for referencing an element of a list is qw(a b c d)[index] # where index starts at 0. <rule> condition = 1 fill_color = eval(qw(dorange orange lorange lblue blue dblue)[remap_int(var(value),-0.6,0.6,0,5)]) </rule>
Recall that you can use
conf() to reference a configuration parameter. This is described in detail in the Automation and Macros tutorial.
In this example, I create a background for the histogram track that has six colored layers: tones of blue for positive values and tones of orange for negative values. Both cutoffs for the layers and colors will be defined as parameters within the <plot> block.
Each separate colored layer in the background is defined by its own <background> block.
<plot> ... # define background color cutoffs bgy1 = 0.2 # first cutoff bgy2 = 0.5 # second cutoff bgc1 = orange # bg color for negative values bgc2 = blue # bg color for positive values ... <backgrounds> # use the parameters above using conf(.,param) <background> color = lconf(.,bgc2) y0 = conf(.,bgy2) </background> <background> color = vlconf(.,bgc2) y1 = conf(.,bgy2) y0 = conf(.,bgy1) </background> <background> color = vvlconf(.,bgc2) y1 = conf(.,bgy1) y0 = 0 </background> <background> color = vvlconf(.,bgc1) y1 = 0 y0 = -conf(.,bgy1) </background> <background> color = vlconf(.,bgc1) y1 = -conf(.,bgy1) y0 = -conf(.,bgy2) </background> <background> color = lconf(.,bgc1) y1 = -conf(.,bgy2) </background> </backgrounds> </plot>
The axis grid can also reference the histogram cutoff values.
<axes> # every 25% with low transparency <axis> color = grey_a1 thickness = 2 spacing = 0.25r # every 5% with higher transparency <axis> color = grey_a3 thickness = 1 spacing = 0.05r </axis> # thick line at y=0 <axis> color = grey_a1 thickness = 5 position = 0 </axis> # at each background cutoff, a thick white line <axis> color = white thickness = 5 position = -conf(.,bgy2),-conf(.,bgy1),conf(.,bgy1),conf(.,bgy2) </axis> </axes>