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1
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2 # This is the main configuration file for the Circos tableviewer. This file also
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3 # depends on colors.conf (definition on basic colors), ideogram.conf (size and spacing of
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4 # row/cell segments), and ticks.conf (tick spacing and label definitions - these are turned
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5 # off by default).
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6 #
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7 # In addition to these configuration files, the bin/make-conf script creates
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8 # colors.conf (colors of row/col segments) and colors_percentile.conf (colors based on
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9 # cell percentile values). These configuration files are also included via the <<include>> directive.
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10 #
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11 # Some elements of the output image are toggled off by default (e.g. row and column highlights,
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12 # anchor links to segment labels, tick marks).
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13
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14 <colors>
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15 <<include DATA_DIR/etc_colors.conf>>
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16 <<include DATA_DIR/colors.conf>>
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17 <<include DATA_DIR/colors_percentile.conf>>
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18 </colors>
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19
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20 <fonts>
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21 <<include DATA_DIR/fonts.conf>>
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22 </fonts>
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23
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24 <<include DATA_DIR/ideogram.conf>>
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25 <<include DATA_DIR/ticks.conf>>
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26
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27 karyotype = DATA_DIR/karyotype.txt
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28
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29 <image>
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30 dir = DATA_DIR
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31 file = circos.png
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32 24bit = yes
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33 svg = no
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34 png = yes
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33
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35 pdf = yes
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36 # radius of inscribed circle in image
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37 radius = 1500p
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38 background = white
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39 # by default angle=0 is at 3 o'clock position
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40 angle_offset = -180
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41 auto_alpha_colors = yes
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42 auto_alpha_steps = 5
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43 </image>
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44
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45 chromosomes_units = 10
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46 chromosomes_display_default = yes
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47 chromosomes_order_by_karyotype = yes
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48
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49 <highlights>
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50
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51 show = yes
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52
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53 <highlight>
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54 show = no
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55 file = DATA_DIR/row.txt
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56 r0 = 1r+200p
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57 r1 = 1r+220p
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58 stroke_color = black
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59 stroke_thickness = 2
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60 </highlight>
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61
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62 <highlight>
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63 show = no
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64 file = DATA_DIR/col.txt
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65 r0 = 1r+230p
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66 r1 = 1r+250p
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67 stroke_color = black
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68 stroke_thickness = 2
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69 </highlight>
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70
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71 <highlight>
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72 show = no
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73 file = DATA_DIR/all.txt
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74 r0 = 1r+10p
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75 r1 = 1r+35p
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76 stroke_color = black
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77 stroke_thickness = 2
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78 </highlight>
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79
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80 </highlights>
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81
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82 <plots>
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83
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84 <plot>
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85 type = text
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86 file = DATA_DIR/segmentlabel.txt
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87 label_font = condensedbold
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88 color = black
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89 label_size = 30p
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90 r0 = 1r+50p
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91 r1 = 1r+500p
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92 rpadding = 0p
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93 padding = 0p
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94
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95 show_links = no
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96 link_dims = 0p,10p,32p,10p,5p
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97 link_thickness = 3p
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98 link_color = black
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99
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100 label_snuggle = no
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101 # shift label up to its height in pixels in the angular direction
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102 max_snuggle_distance = 2r
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103 snuggle_sampling = 2
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104 snuggle_tolerance = 0.25r
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105
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106 </plot>
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107
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108 </plots>
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109
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110 <links>
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111
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112 <link cellvalues>
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113 ribbon = yes
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114 flat = yes
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115 file = DATA_DIR/cells.txt
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116 bezier_radius = 0.0r
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117 radius = 0.999r-15p
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118 thickness = 1
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119 color = grey
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120 stroke_color = black
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121 stroke_thickness = 1
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122 <rules>
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123
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124 <rule>
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125 importance = 95
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126 condition = 1
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127 radius1 = 0.999r+2p
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128 flow = continue
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129 </rule>
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130
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131 </rules>
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132
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133 </link>
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134
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135 </links>
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136
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137 #anglestep = 0.5
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138 #minslicestep = 10
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139 #beziersamples = 40
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140 #debug = no
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141 #warnings = no
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142 #imagemap = no
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143
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144 #units_ok = bupr
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145 #units_nounit = n
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146
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147 <<include DATA_DIR/housekeeping.conf>>
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148
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