#circos -conf circos.conf

<<include /etc/circos/colors_fonts_patterns.conf>>

karyotype = circos_data/karyotype.microbe.txt

chromosomes_units           = 10000
chromosomes_display_default = yes

<ideogram>
show = yes
<spacing>
default = 0.01r
break   = 0.5r  #8r  # Adds a gap between the first and last position of the single chromosome
</spacing>
radius    = 0.9r
thickness = 25p
fill      = no
stroke_thickness = 2
stroke_color     = black
show_bands = yes
fill_bands = yes
band_transparency = 0
show_label       = yes
label_font       = default
label_radius = 1.05r
label_size       = 75
label_parallel   = yes
orientation      = 100 # Rotate the plot by 90 degrees
</ideogram>

#<<include ticks.conf>>
show_ticks          = yes
show_tick_labels    = yes

show_grid          = no
grid_start         = dims(ideogram,radius_inner)-0.5r
grid_end           = dims(ideogram,radius_inner)

<ticks>
skip_first_label     = yes
skip_last_label      = no
radius               = dims(ideogram,radius_outer)
tick_separation      = 2p
min_label_distance_to_edge = 0p
label_separation = 5p
label_offset     = 5p
label_size = 8p
multiplier = 0.001
color = black

thickness = 3p
size      = 20p

<tick>
size           = 10p
spacing        = 1u
color          = black
show_label     = no
label_size     = 12p
format         = %.2f
grid           = no
grid_color     = lblue
grid_thickness = 1p
</tick>
<tick>
size           = 15p
spacing        = 5u
color          = black
show_label     = yes
label_size     = 16p
format         = %s
grid           = yes
grid_color     = lgrey
grid_thickness = 1p

</tick>
<tick>
size           = 18p
spacing        = 10u
color          = black
show_label     = yes
label_size     = 16p
format         = %s
grid           = yes
grid_color     = grey
grid_thickness = 1p
</tick>
<tick>
spacing        = 100u
color          = black
show_label     = yes
suffix = " kb"
label_size     = 36p
format         = %s
grid           = yes
grid_color     = dgrey
grid_thickness = 1p
</tick>
</ticks>

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

<colors>
<<include /etc/circos/colors.conf>>
</colors>

<fonts>
<<include /etc/circos/fonts.conf>>
</fonts>


<plots>
    # -- Scatter plot 1: Intracellular mutants (moved to outermost) --
    <plot>
    type       = scatter
    file       = circos_data/intracellular_mutants.txt
    r1         = 0.95r
    r0         = 0.86r
    min        = 0
    max        = 150000
    glyph      = circle
    glyph_size = 5
    color      = dblue
    <axes>
        <axis>
            spacing   = 50000
            color     = lgrey
        </axis>
    </axes>
    </plot>

    # -- Scatter plot 2: Growthout control --
    <plot>
    type       = scatter
    file       = circos_data/growthout_control.txt
    r1         = 0.85r
    r0         = 0.76r
    min        = 0
    max        = 150000
    glyph      = circle
    glyph_size = 5
    color      = dred
    <axes>
        <axis>
            spacing   = 50000
            color     = lgrey
        </axis>
    </axes>
    </plot>

    # -- Scatter plot 3: LB culture --
    <plot>
    type       = scatter
    file       = circos_data/LB_culture.txt
    r1         = 0.75r
    r0         = 0.66r
    min        = 0
    max        = 150000
    glyph      = circle
    glyph_size = 5
    color      = dpurple
    <axes>
        <axis>
            spacing   = 50000
            color     = lgrey
        </axis>
    </axes>
    </plot>

    # -- Scatter plot 4: Initial mutants --
    <plot>
    type       = scatter
    file       = circos_data/initial_mutants.txt
    r1         = 0.65r
    r0         = 0.56r
    min        = 0
    max        = 150000
    glyph      = circle
    glyph_size = 5
    color      = dyellow
    <axes>
        <axis>
            spacing   = 50000
            color     = lgrey
        </axis>
    </axes>
    </plot>

    # -- Gene Locations: Essential genes heatmap --
    <plot>
    type       = heatmap
    file       = circos_data/merged_genome.txt
    r1         = 0.50r
    r0         = 0.47r
    color      = orange
    </plot>
</plots>

<<include /etc/circos/housekeeping.conf>>