7 — Axis Scaling

1. Global Scale Adjustment

This series of tutorials focuses on adjusting ideogram scale, both globally and locally. By scale I mean the quantity

scale = size/degree

which defines the magnification factor of each ideogram on the image.

By default, if you draw all (or some) of the ideograms using

chromosomes_display_default = yes

all ideograms will have the same magnification. This means that the angles they subtend are proportional to the length of the ideogram. Unless you change the scale locally, this proportionality factor is constant across the entire image.

The first image in this example shows the entire human genome—about 3Gb— fit in 360 degrees. This gives a scale of about 8 Mb/degree. The circumference of the ideogram circle for an 800 x 800 pixel image (the resolution of the images in this example) is about 2000 pixels. When expressed in terms of pixels, the scale is 1.5 Mb/pixel at the radius of the ideograms.

increasing image size

The simplest way to make everything larger is to increase the size of the output image. The best way to do this is to override the radius parameter in the <image> block.

<image>
<<include etc/image.conf>>
radius* = 3000p
</image>

The default value is radius = 1500p, which creates images 3,000 x 3,000 pixels in size. This is generally sufficient (>300 dpi) for images printed at 10 inches or less.

global scale control

Within an image you can adjust the magnification factor of individual ideograms, or groups of ideograms. This is useful to do because genomes tend to be interesting in spots.

You can adjust the length scale for each ideogram using the chromosomes_scale parameter. The parameter associates a magnification with each ideogram. For example,

chromosomes_scale = hs1:0.2;hs2:0.2;hs3:0.2;hs8:5;hs9:5;hs10:5

would result in chromosomes 1, 2, and 3 drawn at 0.2x their size and chromosomes 8, 9, and 10 drawn at 5x. All other ideograms are scaled appropriately so that all elements fit within the circle.

adjusting scale for multiple ideograms

You can individually enumerate the ideograms for which scale should be adjusted, as shown above, or use a regular expression to select more than one ideogram.

For example, to shrink all ideograms matching the regular expression /rn/,

chromosomes_scale = /rn/:0.5

You can combine regular expressions with lists. This will apply a scale of 2x to rn5, with all other rn ideograms shown at 0.5x.

chromosomes_scale = /rn/:0.5;rn5:2

scale-driven display of ticks and tick labels

By defining the tick_separation and label_separation parameters in the <ticks> block, you can supress the display of ticks and their labels in areas where they appear densely. This is useful to help avoid micro-managing tick and label over-crowding.

Another parameter that helps manage tick labels is min_label_distance_to_edge, which controls the display of labels which are too close to the edge of an ideogram. This parameter is useful if ideograms are closely spaced and their edge tick labels start to overlap. You can also use this parameter to effectively hide the first tick label (typically 0).

<ticks>
tick_separation = 3p
label_separation = 10p
min_label_distance_to_edge = 10p
...
</ticks>

toggling ticks by ideogram

When changing the scale of ideograms, you may need to toggle the display of ticks for specific ideograms to keep the image clean. One use case is to show ticks only for the first ideogram, to establish the scale for the image, and then only for subsequent ideograms for which scale changes.

To hide ticks for specific ideograms (e.g. chr9), use chromosomes parameter in the <tick> block

<tick>
chromosomes = -hs9
spacing     = 0.5u
...
</tick>

To display ticks on specific ideograms (e.g. chr9),

<tick>
chromosomes_display_default = no
chromosomes = hs9
spacing     = 0.5u
...
</tick>