Problem with showing ticks in circos plot

[Νικολής Γιαννάκης]

hello. im trying to create a circos plot that will show the links from a specific chromosomic region on chromosome 16 to other regions at the same chromosome in mice (mm).

The thing is that i can create the plot I want but unfortunately the ticks are not shown. I'll put here the different configuration files i have created. any help? any info about solving this issue?

thanks in advance. i also attach the plot i have created.

CIrcos.conf

karyotype          = /data4/home/..,/.../CIRCOS/data/karyotype/karyotype.mouse.mm10.txt

show_links      = yes

show_highlights = yes

# not useful if you're not using ticks or "u" suffix anywhere for values

chromosomes_units  = 1000000

# to explicitly define what is drawn

chromosomes_display_default = no

chromosomes                 = mm16

# scale.conf contains the chromosomes_scale parameter where the scale is determined by

# the length of the segment in original karyo.txt

#

# if you comment this line out, all segments will be of the same size

#<<include scale.conf>>

<links>

<link>

file          = /data4/home/.../tutorials/CIRCOS/VT5/lipids/linkks.v4.txt

ribbon        = no

flat          = yes

radius        = 0.935r

bezier_radius = 0.9r

</link>

</links>

<<include ideogram.conf>>

<<include ticks.conf>>

<image>

<<include etc/image.conf>>

</image>

<<include etc/colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

ticks.conf

show_ticks          = yes

show_tick_labels    = yes

# show_grid         = yes

<ticks>

chromosomes_display_default = no

# no ticks on chromosomes hs1 and hs2

# use with chromosomes_display_default = yes

chromosomes          = mm16

radius               = dims(ideogram,radius_outer)

#label_offset         = 5p

orientation          = out

#label_multiplier     = 1e-2

color                = black

label_size     = 40

spacing        = 100u

size           = 50p

thickness      = 2p

show_label     = yes

tick_separation      = 15p

</ticks>

ideogram.conf

<ideogram>

show_bands = yes

fill_bands = yes

band_transparency = 4

<spacing>

default = 0.1r

</spacing>

# Ideogram position, fill and outline

radius           = 0.68r

thickness        = 50p

fill             = yes

stroke_color     = dgrey

stroke_thickness = 2p

# Minimum definition for ideogram labels.

show_label       = yes

# see etc/fonts.conf for list of font names

label_font       = default

label_radius     = dims(image,radius) - 430

#label_radius    = (ideogram,radius_outer) + 0.075r

label_size       = 60

label_parallel   = no

#<<include ideogram.position.conf>>

#<<include ideogram.label.conf>>

#<<include bands.conf>>

</ideogram>

I would really appreciate your help.

Kind regards,

Nikolas

[Martin Krzywinski]

Your ticks are not showing because your ticks.conf file and contents of <ticks> block is incorrectly formatted.

You need at least one <tick> block that defines tick spacing.

http://www.circos.ca/documentation/tutorials/ticks_and_labels/basics/

Please see the ticks file in the attached template as a guide.

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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