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.

7 — 2D Data Tracks

2. Line Plots

The line plot differs from the scatter plot in that there are no glyphs drawn at each point position. Rather the points are joined by a line.

The line plot is formatted very similarly to the scatter plot, with the following differences.

  • type=line
  • no glyphs - there are no glyph parameters - glyph and glyph_size do not apply.
  • stroke_thickness and stroke_color are replaced by thickness and color, since the line isn't really outlined
  • adjacent points whose distance is greater than max_gap are not joined by a line - this is useful to avoid drawing lines across large gaps (e.g. centromere) in data

Points that fall outside of the min/max data range are placed at the min/max extremes. Thus, if you have many adjacent points that fall outside the data range the connecting line may run along the bottom or top of the plot track.

If you want to explicitly remove these points from the data set, use a rule that sets show=no. For example, if your min/max values are 0/0.5, then this rule set will remove points falling outside the range from influencing how the connecting line is drawn. 

<rules>
<rule>
condition  = var(value) < 0 || var(value) > 0.5
show       = no
</rule>
</rules>