circos -session 1 Lesson 12 Relative and Absolute Ticks

#../../etc/ideogram.conf  the following are the default settings. Here for the convenience of comparing the default settings and the new settings with suffix * difference, some unrelated settings are commented with double #
# Default ideogram settings for all lessons in this section.

# thickness and color of ideograms
##thickness        = 25p
##stroke_thickness = 1
##stroke_color     = vdgrey

# the default chromosome color is set here and any value
# defined in the karyotype file overrides it
##fill             = yes
##fill_color       = black

# fractional radius position of chromosome ideogram within image
radius         = 0.80r
show_label     = yes
label_font     = default
label_radius   = dims(ideogram,radius) + 0.150r
label_size     = 36

label_parallel = yes
label_case     = upper

# show_bands determines whether the outline of cytogenetic bands
# will be seen
##show_bands            = yes

# in order to fill the bands with the color defined in the karyotype
# file you must set fill_bands
##fill_bands            = yes
##band_stroke_thickness = 1
##band_transparency     = 1

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"ideogram.conf" 32L, 857C                                                                                                                   11,1          All

#./etc/ideogram.conf
<ideogram>

<spacing>
default = 10u
</spacing>

<<include ../../etc/ideogram.conf>>
# the suffix indicates that the corresponding parameter values should override any previously seen definitions of thos parameter. we can employ multiple levels of overiding parameters,by using more than one "*" in the suffix.
label_radius*          = dims(ideogram,radius) + 0.3r
band_stroke_thickness* = 1
band_stroke_color*     = black
band_transparency*     = 5

stroke_thickness*      = 1

label_format = eval(sprintf("%s",var(chr)))
</ideogram>

~                   

there are several paraments that end  in " * ". This suffix indicates that the corresponding parameter values should override any previously seen definitions of this parameter.  you can employ multiple levels of overriding parameters, by using more than one " * " in the suffix. Thus, Label_radius will be overridden by Label_radius*, which will be overridden by Label_radius**, and so on.

 

here we redefine  stroke_thickness** = 10   band_stroke_thickness** = 10 

<ideogram>

<spacing>
default = 10u
</spacing>

<<include ../../etc/ideogram.conf>>

label_radius*          = dims(ideogram,radius) + 0.3r
band_stroke_thickness* = 1
band_stroke_thickness** = 10
band_stroke_color*     = black
band_transparency*     = 5

stroke_thickness*      = 1
stroke_thickness**     =10
label_format = eval(sprintf("%s",var(chr)))
</ideogram>

figure

#1/12/etc/ticks.conf
grid_start     = 1r
grid_end       = 1r+45p
grid_color     = grey
grid           = yes
</tick>

<tick>
spacing        = 2u
size           = 3p
thickness      = 2p
show_label     = no
</tick>

<tick>
radius         = 0.75r
spacing_type   = relative
rspacing       = 0.02
size           = 3p
thickness      = 1p
show_label     = no
</tick>

<tick>
radius         = 0.75r
spacing_type   = relative
rspacing       = 0.10
size           = 6p
thickness      = 1p
show_label     = yes
label_relative = yes
rmultiplier    = 100
suffix         = %

grid_start     = 0.5r
grid_end       = 0.75r
grid_color     = grey
grid           = yes

</tick>

</ticks>
                                                                                                                                            75,1          Bot

surprise 1 

figure

#the master ? if the parameter show_tick_labels= no ,does <tick> <show_label> still #work ?
show_ticks        = yes
show_tick_labels  = no
show_grid         = yes

<ticks>
label_font      = default
radius          = dims(ideogram,radius_outer) + 45p
label_offset    = 5p
label_size      = 8p
multiplier      = 1e-6
color           = black
format          = %d
grid_thickness  = 1p
<tick>
spacing        = 20u
size           = 12p
thickness      = 2p
show_label     = yes
label_size     = 10p

grid_start     = 1r
grid_end       = 1r+45p
grid_color     = vdgrey
grid           = yes
</tick>

figure

 surprise 2

show_ticks        = no
show_tick_labels  = yes
show_grid         = yes

figure

 

define the highlight regions   

#chr start end optons
hs1 0 249250621 fill_color=rdylbu-11-div-2
hs2 0 243199373 fill_color=rdylbu-11-div-3
mm1 0 197195432 fill_color=rdylbu-11-div-10
mm2 0 181748087 fill_color=rdylbu-11-div-9

                                                                                                                                                         

Figure 41

what if I comment the highlight  , and  show_grid = no 

#.1/12/etc/circos.conf
karyotype = data/karyotype/karyotype.human.txt,data/karyotype/karyotype.mouse.txt

chromosomes_units           = 1000000
chromosomes_display_default = no

chromosomes         = hs1;hs2;mm1;mm2
chromosomes_order   = hs1,hs2,mm2,mm1
chromosomes_color   = hs1=rdylbu-11-div-2,hs2=rdylbu-11-div-3,mm1=rdylbu-11-div-10,mm2=rdylbu-11-div-9

chromosomes_reverse = mm1,mm2
chromosomes_scale   = /./=1rn

#<highlights>
#<highlight>
#file = ../data/highlight.txt
#r0   = 1r+40p
#r1   = 1r+45p
#</highlight>
#</highlights>

<<include ideogram.conf>>

<<include ticks.conf>>

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

<<include etc/colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

#1/12/etc/ticks.conf
show_ticks        = yes
show_tick_labels  = yes
show_grid         = no

 

 

Figure

Congratulations !  Have  Finished the session 1