7 — Axis Scaling

8. Drawing Data with Scale Adjustment

circos.conf

<<include etc/colors_fonts_patterns.conf>>

<ideogram>
radius* = 0.8r
</ideogram>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype = data/karyotype/karyotype.human.txt

<image>
<<include etc/image.conf>>
</image>

chromosomes_units           = 1000000
chromosomes_display_default = no

chromosomes                 = hs1;hs2
#chromosomes                = hs1[a]:0-0.8;hs1[b]:16.6-17.2;hs1[c]:141.5-148;hs1[d]:220.6-222.4;hs2[e]:90.8-95.2;hs2[f]:132.3-132.8;hs2[g]:242.5-)
#chromosomes_breaks = -hs1:142.3-143.9;-hs1:144.2-144.7;-hs1:145-146;-hs1:220.8-222;-hs2:91.8-94.6

<zooms>
smooth_distance = 1r
smooth_steps    = 40
<zoom>
chr = hs1
start = 0u
end = 0.5u
scale = 120
</zoom>
<zoom>
chr = hs1
start = 16.7u
end = 17u
scale = 200
</zoom>
<zoom>
chr = hs1
start = 20u
end = 100u
scale = 0.1
</zoom>
<zoom>
chr = hs1
start = 144u
end = 145u
scale = 20
</zoom>
<zoom>
chr = hs1
start = 160u
end = 195u
scale = 0.1
</zoom>
<zoom>
chr = hs2
start = 10u
end = 80u
scale = 0.1
</zoom>
<zoom>
chr = hs2
start = 89.5u
end = 110u
scale = 10
</zoom>
<zoom>
chr = hs2
start = 87.2u
end = 87.8u
scale = 40
</zoom>
<zoom>
chr = hs2
start = 90.5u
end = 92u
scale = 40
</zoom>
<zoom>
chr = hs2
start = 93u
end = 103u
scale = 0.02
</zoom>
<zoom>
chr = hs2
start = 109.5u
end = 112.5u
scale = 20
</zoom>
<zoom> 
chr = hs2
start = 115u
end =  240u
scale = 0.1
</zoom>
</zooms>

<links>

radius = 0.99r
crest  = 1
color  = grey
bezier_radius        = 0r
bezier_radius_purity = 0.5

<link>
file         = data/5/segdup.txt
ribbon       = yes
thickness    = 2
stroke_color = vdgrey
stroke_thickness = 2

<rules>

flow = continue

<rule>
condition  = var(intrachr)
condition  = abs(var(pos1) - var(pos2)) < 10Mb
show       = no
</rule>

<rule>
condition  = max(var(size1),var(size2)) < 5000
show       = no
</rule>

<rule>
condition  = 1
z          = eval(int(max(var(size1),var(size2))/5000))
</rule>

<rule>
condition    = var(intrachr) 
condition    = (var(chr1) eq "hs1" && var(start1) < 1Mb) || (var(chr2) eq "hs1" && var(start2) < 1Mb)
color        = orange
stroke_color = dorange
</rule>

<rule>
condition    = var(intrachr) 
condition    = (var(chr1) eq "hs1" && var(start1) > 16Mb && var(start1) < 17Mb) || (var(chr2) eq "hs1" && var(start2) > 16Mb && var(start2) < 17Mb)
color        = lblue
stroke_color = dblue
</rule>

</rules>

</link>

</links>

<plots>
<plot>
type  = heatmap
file  = data/7/heatmap.zoom-06.txt
r1    = 1.16r
r0    = 1.12r
color = spectral-9-div
stroke_thickness = 0
scale_log_base   = 0.5
</plot>
</plots>

<<include etc/housekeeping.conf>>
data_out_of_range* = trim

bands.conf

show_bands            = no
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 3

breaks.conf

axis_break_at_edge = yes
axis_break         = yes
axis_break_style   = 2

<break_style 1>
stroke_color     = black
fill_color       = blue
thickness        = 0.25r
stroke_thickness = 2
</break_style>

<break_style 2>
stroke_color     = black
stroke_thickness = 2
thickness        = 2r
</break_style>

ideogram.conf

<ideogram>

<spacing>
default = 0.005r
break   = 0.5r

<<include breaks.conf>>

</spacing>

<<include ideogram.position.conf>>
<<include ideogram.label.conf>>
<<include bands.conf>>

</ideogram>

ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = dims(image,radius) - 50p
label_size       = 36
label_parallel   = yes
label_case       = lower
label_format     = eval(sprintf("chr%s",var(label)))

ideogram.position.conf

radius           = 0.90r
thickness        = 50p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

ticks.conf

show_ticks          = yes
show_tick_labels    = yes

<ticks>
label_separation = 10p
tick_separation  = 3p
radius           = dims(ideogram,radius_outer)
multiplier       = 1e-6
label_offset     = 0p
color            = black

<tick>
spacing        = 0.02u
size           = 5p
thickness      = 2p
show_label     = no
label_size     = 12p
format         = %.1f
</tick>

<tick>
spacing        = 0.1u
size           = 8p
thickness      = 2p
show_label     = yes
label_size     = 12p
format         = %.1f
</tick>

<tick>
spacing        = 0.5u
size           = 10p
thickness      = 2p
show_label     = yes
label_size     = 12p
format         = %.1f
</tick>

<tick>
spacing        = 1u
size           = 12p
thickness      = 2p
show_label     = yes
label_size     = 12p
format         = %d
</tick>

<tick>
spacing        = 5u
size           = 14p
thickness      = 2p
show_label     = yes
label_size     = 16p
format         = %d
</tick>

<tick>
spacing        = 10u
size           = 18p
thickness      = 2p
show_label     = yes
label_size     = 20p
label_offset   = 5p
format         = %d
</tick>

</ticks>