Circos > Documentation > Tutorials > Recipes > Stacked Histograms
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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.

Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.

8 — Recipes

8. Stacked Histograms

circos.conf


<<include etc/colors_fonts_patterns.conf>>

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

karyotype   = data/karyotype/karyotype.human.txt

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

chromosomes_units           = 1000000
chromosomes                 = /hs[1-3]$/
chromosomes_display_default = no

<plots>

<plot>

file = data/8/histogram.stacked.txt
type = histogram
r0   = 0.6r
r1   = 0.95r
min  = 0
max  = 5

color      = white
fill_color = red,orange,yellow,green,blue
#fill_color = grey,grey,grey,black,black
#pattern    = vline,hline,solid,checker,solid
thickness  = 2
#thickness  = 1,5,10,15,20

sort_bin_values = no
extend_bin      = no

<axes>
<axis>
color     = lgrey
thickness = 2
spacing   = 0.1r
</axis>
</axes>

</plot>

</plots>

<<include etc/housekeeping.conf>>



bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 3


ideogram.conf


<ideogram>

<spacing>
default = 0.005r
break   = 0.5r

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>

<break_style 2>
stroke_color     = black
stroke_thickness = 2
thickness        = 1.5r
</break>

</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        = 30p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black


ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>
tick_separation      = 3p
label_separation     = 5p
radius               = dims(ideogram,radius_outer)
multiplier           = 1e-6
color          = black
size           = 20p
thickness      = 4p
label_offset   = 5p
format         = %d

<tick>
spacing        = 1u
show_label     = yes
label_size     = 16p
</tick>

<tick>
spacing        = 5u
show_label     = yes
label_size     = 18p
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 20p
</tick>

<tick>
spacing        = 20u
show_label     = yes
label_size     = 24p
</tick>

</ticks>