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.

5 — Tick Marks, Grids and Labels

3. Tick Marks - Label Margins

If your tick marks are densely spaced, their labels may overlap and lose their legibility. Like the tick mark margin parameter, tick label margins help you suppress labels that might overlap.

A tick label will not be drawn if its tick mark is not drawn. Thus, a natural way to suppress labels is to suppress the tick marks. This is done using tick_separation and is described in the previous tutorial.

Label separation is controlled independently using label_separation. Like tick_separation, the label_separation parameter defines a minimum allowed distance between labels. Labels closer than this distance to another label will not be drawn. Also, as with tick marks themselves, label overlap is checked within a tick mark group (i.e. 1u and 5u labels are compared for overlap). 

<ticks>

  tick_separation  = 2p
  label_separation = 5p
  ...

  <tick>
  tick_separation  = 5p
  label_separation = 10p
    ...
  </tick>

  ...

</ticks>

The mechanics behind label margins work exactly the same way as tick mark margins. For example, you can define label_separation globally or within individual <tick> blocks.

Overlap is calculated in the angular direction only. Any tick label offset does not change the way overlap is calculated, a process in which the radial position of the label is disregarded. By introducing label offsets (shifting labels of tick mark sets radially) you can effectively eliminate overlap without supressing ticks. This is covered in the next section.

If you want to turn off label overlap check for a given tick mark group, set label_separation=0p.

minimum label distance to ideogram edge

To suppress tick labels near the edge of the ideogram, use min_label_distance_to_edge. This parameter can be used globally in the <ticks> block to affect all ticks, or locally with a <tick> block to affect an individual tick group. 

<ticks>
min_label_distance_to_edge = 10p
...
<tick>
min_label_distance_to_edge = 5p
...
</tick>
...
</ticks>

The corresponding parameter to suppress ticks near an ideogram edge is min_distance_to_edge. If the tick mark is suppressed with this parmaeter then no label is shown.

suppressing first or last label of a group

You can suppress the label of the first tick, or last tick, in a group using skip_first_label and skip_last_label. 

<ticks>
skip_first_label = yes
skip_last_label  = yes
...
<tick>
# will overwrite the skip_first_label for this tick group
skip_first_label = no
...
</tick>
...
</ticks>

The purpose of this parameter is to reduce label clutter near the edges of the ideogram. The effect is similar to using min_label_distance_to_edge, which was described above, but skip_*_label affects at most one label.

The mechanics of the first/last label suppression is applied on a group-by-group basis. Thus, if skip_last_label is set for all tick groups, the last label for each group will be suppressed, and not the last label on the ideogram.