<<include etc/colors_fonts_patterns.conf>>  # 导入配置文件：颜色
<<include etc/housekeeping.conf>>  ## 导入管家参数

show_ticks          = yes
show_tick_labels    = yes

<ticks>
skip_first_label = no
skip_last_label  = no
radius           = dims(ideogram,radius_outer)
tick_separation  = 2p
label_separation = 5p
multiplier       = 1
color            = black
thickness        = 4p
size             = 20p

<tick>
spacing        = 1u
show_label     = yes
thickness      = 2p
#color          = dgrey
color          = black
label_size     = 20p
label_offset   = 10p
grid           = yes
grid_thickness = 1p
grid_start     = 0.5r
grid_end       = 0.999r
</tick>

</ticks>


<image>
    # <<include etc/image.conf>>
    dir   = /var/www/cloud_workdir/pipelines/957/mix_binning_eT8TqvLowaxhNro3gqEnsT/cb_visualizeh5nAbuZaBGX8m39bHFeiKr_result/06-MAG_Circos/MAG.T2.198/
    file  = circos.png
    png   = yes
    svg   = yes
    background = white
    # radius of inscribed circle in image
    radius  = 1500p
    angle_offset      = -90
    auto_alpha_colors = yes
    auto_alpha_steps  = 5
</image>

karyotype = karyotype.txt
chromosomes_units = 10000  # 指定距离单位u
chromosomes_display_default = yes  # 显示所有的染色体(no的话需要自己指定)

# 1. 第一圈：染色体

<ideogram>

    <spacing>
        default = 0.005r
        # 设置圈图中染色体之间的空隙大小，我们设置为0.005r的意思是每个染色体之间的空隙占周长0.5%

    </spacing>

    radius = 0.8r  # 圈半径
    thickness = 50p  # 圈厚度
    fill = yes  # 圈颜色
    # stroke_color = 160,32,240  #染色体外边框轮廓颜色
    # stroke_thickness=2p  #轮廓厚度
    show_label       = yes
    label_font       = default
    label_radius     = 1.1r
    label_with_tag   = yes
    label_size       = 30
    label_parallel   = yes
    label_color      = black
</ideogram>

# 2. 第二圈：正义、反义、CDS

<highlights>
    z = 0
    <highlight>
        file = strand.txt
        r0 = 0.96r
        r1 = 0.99r
    </highlight>
    <highlight>
        file = annotation.txt
        r0 = 0.80r
        r1 = 0.84r
    </highlight>
</highlights>


<plots>
thickness = 1p

# 3. 第三圈：tRNA

    <plot>
        show = yes
        type = scatter  # 类型：scatter/line/histogram/heatmap

        file = type.txt
        radius = 0.88r
        r0 = 0.88r
        r1 = 0.92r
        max = 1.0
        min = 0.0

        glyph = triangle  # 类型：circle/triangle/rectangle
        glyph_size = 20  # 大小
        # color = 0,0,255  # 无影响
        # fill_color = 0,0,255  # 填充色：红色
        # stroke_color = 0,0,255  # 边框色：红色
        # stroke_thickness = 1
    </plot>
    # GC content
    <plot>
        type = histogram
        z = 2
        max_gap = 0u
        file = gc_content.txt
        # color = orange
        # fill_color = 255,97,0  # 橙色
        r0 = 0.50r
        r1 = 0.70r
        # orientation = out  # 朝外
    </plot>
    # GC skew
    <plot>
        type = histogram
        z = 2
        max_gap = 0u
        file = gc_skew.txt
        # color = orange
        # fill_color = 255,97,0  # 橙色
        r0 = 0.29r
        r1 = 0.49r
        # orientation = out  # 朝外
    </plot>
</plots>