6 — 2D Data Tracks

5. Heat maps

circos.conf

<<include etc/colors_fonts_patterns.conf>>

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

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

karyotype   = data/karyotype/karyotype.human.txt

chromosomes_units  = 1000000
chromosomes        = hs1;hs2
chromosomes_breaks = -hs1:120-140
chromosomes_display_default = no

track_width = 0.05
track_pad   = 0.02
track_start = 0.95

<plots>

type    = heatmap

# default file for all tracks
file             = data/6/snp.number.1mb.txt

# a 9 color diverging spectral palette specified using a color list name
color  = spectral-9-div

# referenced via conf(plots,color_alt)
color_alt = black,spectral-8-div,grey

# or the reverse list
#color = spectral-9-div-rev

# or you can even combine lists
# color = ylorrd-9-seq-rev,ylgnbu-9-seq

stroke_thickness = 1
stroke_color     = black
min              = 1000
max              = 5000

<plot>
<<include r0r1.conf>>
file             = data/6/variation.heatmap.txt
stroke_thickness = 0
min              = 2000
max              = 250000
</plot>

<plot>
<<include r0r1.conf>>
scale_log_base   = 0.5
</plot>

<plot>
<<include r0r1.conf>>
scale_log_base   = 1   # this is the default value
</plot>

<plot>
<<include r0r1.conf>>
scale_log_base   = 2
</plot>

<plot>
<<include r0r1.conf>>
scale_log_base   = 3
</plot>

<plot>
<<include r0r1.conf>>
scale_log_base   = 5
</plot>

<plot>
<<include r0r1.conf>>
color            = conf(plots,color_alt)
file             = data/6/heatmap.step.txt
pattern          = hline,vline
color_mapping    = 0  # default
min              = 0
max              = 10
stroke_thickness = 0
</plot>

<plot>
<<include r0r1.conf>>
color            = conf(plots,color_alt)
file             = data/6/heatmap.step.txt
pattern          = hline,solid,vline
color_mapping    = 1
min              = 0
max              = 10
stroke_thickness = 0
</plot>

<plot>
<<include r0r1.conf>>
color            = conf(plots,color_alt)
file             = data/6/heatmap.step.txt
pattern          = hline,solid,vline
color_mapping    = 2
min              = 0
max              = 10
stroke_thickness = 0
</plot>

<plot>
<<include r0r1.conf>>
color            = conf(plots,color_alt)
file             = data/6/heatmap.step.txt
pattern          = hline,checker,vline
color_mapping    = 2
min              = 2
max              = 8
stroke_thickness = 0
</plot>

</plots>

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

bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 0

ideogram.conf

<ideogram>

<spacing>
default = 0.01r
break   = 0.5r
</spacing>

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

radius*       = 0.825r

</ideogram>

ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = dims(image,radius)-30p
label_size       = 24
label_parallel   = yes
label_case       = lower
label_format     = eval(sprintf("chr%s",var(label)))

ideogram.position.conf

radius           = 0.775r
thickness        = 30p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

r0r1.conf

# set track radius values based on track counter
r1  = eval(sprintf("%fr",conf(track_start)-counter(plot)*(conf(track_width)+conf(track_pad))))
r0  = eval(sprintf("%fr",conf(track_start)-counter(plot)*(conf(track_width)+conf(track_pad))-conf(track_width)))

ticks.conf

show_ticks          = yes
show_tick_labels    = yes

<ticks>

radius           = dims(ideogram,radius_outer)
orientation      = out
label_multiplier = 1e-6
color            = black
size             = 20p
thickness        = 3p
label_offset     = 5p
format           = %d

<tick>
spacing        = 1u
show_label     = no
size           = 10p
</tick>

<tick>
spacing        = 5u
show_label     = yes
label_size     = 20p
size           = 15p
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 24p
</tick>

</ticks>