Circos > Documentation > Tutorials > Ideograms > Spacing Breaks

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3 — Drawing Ideograms

6. Spacing and Axis Breaks

ideogram spacing

Spacing between ideograms derived from different chromosomes is controlled by the default parameter in <ideogram><spacing> block.

absolute spacing

This parameter may be set relative to chromosome units (suffixed with u). For example, if chromosomes_units=1000000 and the spacing value is 10u, then the actual spacing in the image will be 10Mb. 

<ideogram>
 <spacing>
  default = 10u
 </spacing>
</ideogram>

relative spacing

You can also set the parameter to be relative to the total size of ideograms in the image (suffix with r). This is useful if you would like to maintain a fixed spacing between ideograms as you add/remove ideograms from the image. 

<ideogram>
 <spacing>
  default = 0.01r
 </spacing>
</ideogram>

In this example, the spacing will be 1% of the size of all ideograms. This will be close to 1% of the circumference of the image.

Use the absolute value format (e.g. 10u), when you have created your ideogram layout and want to adjust the spacing value to be visually compatible with adjacent tick marks. For example, if you have major ticks every 5Mb, you may want to set the spacing value to this.

Use the relative value format (e.g. 0.01r), when you anticipate that you will be adding/removing/cropping ideograms from the image but do not want the spacing value to fluctuate.

changing spacing between specific ideograms

Spacing between specific ideograms can be adjusted in <pairwise> block. 

<ideogram>
 <spacing>
  default = 10u

  <pairwise hs1>
   spacing = 5u
  </pairwise>

  <pairwise hs3 hs4>
   spacing = 0.25r
  </pairwise>

 </spacing>
</ideogram>

When you specify the name of one ideogram, spacing on either side of it will be affected. The first pairwise block creates 5u spacing around hs1.

When you specify the names of two ideograms, the spacing between them is affected. If you use relative spacing, it is interpreted to be relative to the default spacing. Thus, spacing=0.25r between hs3 and hs4 will be 2.5u (i.e. 25% of 10u).

making room for a legend

To make room for a track legend, use the <pairwise> block to adjust spacing between the ideograms at the top of the image and then angle_offset to rotate the image to center the spacing along the vertical line. 

# ideogram.conf
<ideogram>
 <spacing> 
  # spacing between ideograms is 0.1% of image
  default = 0.001r 

  <pairwise hsY hs1>
   # spacing between hsY and hs1 is 50x 0.1% of image
   spacing = 50r 
  </pairwise>

 </spacing>
</ideogram>

# circos.conf
<image>
 # override angle_offset defined in etc/image.conf 
 angle_offset* = -82
 <<include etc/image.conf>>
</image>

This example assumes that hsY and hs1 are the last and first ideograms in your image, flanking the 12 o'clock position.

By default, angle_offset=-90, which makes ideograms start at 12 o'clock position. The image is rotated slightly clockwise by reducing this offset. You'll need to determine this offset yourself—start at -85 and then vary the value up/down as required.

axis breaks

When only a subregion of a chromosome is drawn, you have the option to place axis breaks on the ideogram to indicate that the chromosome extent is larger than shown in the figure.

There are two axis break styles, with style properties defined in break_style blocks. The size of the axis break is controlled by the break parameter and can be defined in absolute units (u) or relative to the default spacing (r). 

<ideogram>
  block(spacing>

  default = 10u
  break   = 2u

  axis_break         = yes
  axis_break_style   = 2
  axis_break_at_edge = yes

  <break_style 1>
    stroke_color = black
    fill_color   = blue
    thickness    = 0.25r
    stroke_thickness = 2
  </break_style>

  <break_style 2>
    stroke_color     = black
    stroke_thickness = 3
    thickness        = 1.5r
  </break_style>

  </spacing>
</ideogram>

If an ideogram does not begin at its chromosome start or end, you can choose to place an axis break at the edge with axis_break_at_edge=yes.

The thickness parameter defines the radial extent of the break and can be expressed relative to the thickness of the ideogram (e.g. 0.25r) or in in absolute pixel size (e.g. 100p). Typically, break style 1 should have a thickness <1r and style 2 should have a thickness >1r.

The axis break defined by style 1 uses a rectangle to join the ideogram across the break. Style 2 uses two radial lines to indicate a break. The size of the break is independent of spacing between two ideograms. Thus, if two neighbouring ideograms have breaks at neighbouring ends, then the total space between them is the sum of break sizes and ideogram spacing.