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 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.
stroke_colorare replaced by
color, since the line isn't really outlined
max_gapare 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
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>