2 — Drawing Ideograms

9. Labels

Each ideogram has a label field in the karyotype file

#
# A name of chromosome used in coordinate files
# B label of chromosome and derived ideograms
#
#     A    B
chr - hs12 12 0 132349534 green

This label field defines the text that is shown in the figure. This text is optional and can be positioned and formatted flexibly.

ideograms vs chromosomes

Keep the difference between chromosomes and ideograms in mind. The chromosome is the structure on which you define position of data. The ideogram is the visual representation of the chromosome or a region of a chromosome.

Most of the time, each chromosome will have one ideogram. However, if you use axis breaks and suppress the display of a region of a chromosome, a chromosome will have more than one ideogram.

When chromosomes are broken up into multple ideograms, each ideogram is identified by a tag (e.g. a, b, c). You can have this tag added to the label.

fonts

Circos supports True Type and Open Type fonts. These fonts are defined in the <font> block. In all of the tutorials this definition is included via the colors_fonts_patterns.conf file, which defines <fonts>, <colors> and <patterns> blocks.

# circos.conf
<<include colors_fonts_patterns.conf>>
...

The <font> block is used to associate a font file (.TTF or .OTF) with a unique name, such as "normal", "bold", "condensed". For example,

light          = fonts/modern/cmunbmr.otf
normal         = fonts/modern/cmunbmr.otf
default        = fonts/modern/cmunbmr.otf
semibold       = fonts/modern/cmunbsr.otf
bold           = fonts/modern/cmunbbx.otf
italic         = fonts/modern/cmunbmo.otf
bolditalic     = fonts/modern/cmunbxo.otf
italicbold     = fonts/modern/cmunbxo.otf

To use the font, specify it by using its definition (e.g. light), not the font file name (e.g. fonts/modern/cmunbmbr.otf). If you specify a font definition that has not been defined, default is used. It's a good idea to always have a default definition.

ideogram labels

Ideogram labels are controlled by these parameters within the <ideogram> block.

<ideogram>
show_label     = yes
label_with_tag = yes
label_font     = light
label_radius   = dims(ideogram,outer_radius) + 0.05r
label_center   = yes
label_size     = 48p
label_color    = grey
label_parallel = yes
label_case     = upper 
label_format   = eval(sprintf("chr%s",var(label)))
...
</ideogram>

label tags

The label_with_tag parameter controls whether a tag associated with the ideogram region is included with the label. Tags are used to identify ideograms from the same chromosome

# tags "a" and "b"
chromosomes = hs1[a]:50-75,hs1[b]:100-125

label font

The label_font specifies the name of the font (using its label, as defined in the <fonts> block.

label position

The label_radius controls the radial position of the ideogram label. Here, it is best to put the label relative to the ideogram outer (or inner) radius. If you would like the label to be centered at this radius, use label_center = yes. A few examples are

# 50 pixels outside the outer ideogram radius
label_radius = dims(ideogram,radius_outer) + 50p

# 5% of inner radius outside outer ideogram radius
label_radius = dims(ideogram,radius_outer) + 0.05r

# inside ideogram
label_radius = (dims(ideogram,radius_outer)+dims(ideogram,radius_inner))/2

# 100 pixels inside the ideogram radius
label_radius = dims(ideogram,radius_inner) - 100p

# 50 pixels inside the image radius
label_radius = dims(image,radius) - 50p

label orientation

You can make the baseline of the ideogram labels to be parallel to the circle by using the label_parallel parameter within the ideogram block.

label case

To override the way the label is displayed, you can force upper or lower case with label_case, which can be set to upper or lower.

# ideogram labels will be uppercase
label_case = upper

label format

You can define the format of the label flexibly by using sprintf. Here, the label of the chromosome (e.g. 1) is prefixed with the string "chr".

label_format = eval(sprintf("chr%s",var(label)))