Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
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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.
9 — Recipes
6. Manipulating Histograms
mapping value to histogram fill
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>
layered background color and macros
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>
y-axis grid and macros
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>