Circos Plots: Tick Marks - Basics

Excerpts from  Tick Marks, Grids and Labels

"Ticks, tick labels and grids are defined in the <ticks> block, which can contain any number of <tick> blocks, each defining ticks with a different spacing."

"Ticks refers to the radial lines that show progression of distance along the ideogram. Tick labels are the accompanying text elements that mark the position of the tick."

"The radius specifies the radial position of the tick marks, which you generally want to set to the outer ideogram radius."

"The label multiplier is the constant used to multiply the tick value to obtain the tick label. For example, if the multiplier is 1e-6, then the tick mark at position 10,000,000 will have a label of 10. The multiplier is applied to the raw tick value, regardless of the value of chromosomes_unit."

"The orientation controls whether the ticks and labels face out (orientation=out) or in (orientation=in)."

"By referencing the position relative to the image, and not the ideogram, you decouple the position of the tick from the position of the ideogram. This absolute placement is useful if you know you want the ticks at a specific image position, regardless of the position of the ideograms. radius=dims(image,radius)-25p."

"Typically, one defines several sets of ticks by using <tick> blocks. Each set defines the display of ticks at a given spacing. For example, one could have three sets of ticks spaced at 1Mb, 5Mb and 10Mb, respectively, and formatted so that the 1Mb ticks are small and without labels whereas the 5Mb and 10Mb be larger and with labels. The 10Mb ticks might use a bolder font, for example, to give them greater visual weight."

"Unless force_display is set for a tick set, ticks at smaller spacing are not drawn at a position that already has another tick. In other words, the formatting of a tick mark is defined by the block associated with the spacing value that defines the largest divisor of the tick value."

"When tick size is expressed in relative terms, the comparator is the tickness of the ideogram. Therefore ticks with size=0.1r will have a length that is 1/10th of the ideogram thickness. Tick thickness, on the other hand, uses the tick size as the comparator. Thus, ticks with thickness=0.1r will have a width that is 1/10th the size of their length. Similarly, if tick label size is defined relatively, it will be scaled by tick size."

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When chromosomes_display_default=yes, you do not need to define which ideograms ticks appear on because tick mark visibility is on by default and you only need to define where tick marks are not shown. If chromosomes_display_default=no, then things get a little bit more complicated, because you now need to define where tick marks will be shown and these definitions can contain regions of exclusion."