time | calls | line |
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| 1 | 1 | colorNoData = [1.0 1.0 1.0 ]; % used when no data is available for the bin.
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| 1 | 2 | colorInit = [0.5 0.5 0.5 ]; % external; used in blending at ends of chr.
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| 1 | 3 | colorHET = [0.66667 0.66667 0.66667]; % near 1:1 ratio SNPs
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| 1 | 4 | colorHOM = [1.0 0.0 0.0 ]; % Hom SNPs;
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| | 5 |
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| 1 | 6 | if (useHapmap == true)
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| | 7 | %% Load color names defined for hapmap;
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| | 8 | colorsFile = [hapmapDir 'colors.txt'];
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| | 9 | if (exist(colorsFile,'file') == 2)
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| | 10 | colors_fid = fopen([main_dir 'users/' hapmapUser '/hapmaps/' hapmap '/colors.txt'], 'r');
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| | 11 | % The swapped colors are to correct for a polarity mistake in the python preprocessing steps.
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| | 12 | % correcting the error there would require reprocessing all current datasets.
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| | 13 | colorA_string = fgetl(colors_fid);
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| | 14 | colorB_string = fgetl(colors_fid);
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| | 15 | fclose(colors_fid);
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| | 16 | else
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| | 17 | colorA_string = 'red';
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| | 18 | colorB_string = 'red';
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| | 19 | end;
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| | 20 | fprintf(['\nHapmap colors:\n\tcolorA = ' colorA_string '\n\tcolorB = ' colorB_string '\n\n']);
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| | 21 | switch colorA_string
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| | 22 | case 'deep pink'
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| | 23 | homolog_a_color = [1.0 0.0 0.5];
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| | 24 | case 'magenta'
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| | 25 | homolog_a_color = [1.0 0.0 1.0];
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| | 26 | case 'electric indigo'
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| | 27 | homolog_a_color = [0.5 0.0 1.0];
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| | 28 | case 'blue'
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| | 29 | homolog_a_color = [0.0 0.0 1.0];
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| | 30 | case 'dodger blue'
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| | 31 | homolog_a_color = [0.0 0.5 1.0];
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| | 32 | case 'cyan'
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| | 33 | homolog_a_color = [0.0 1.0 1.0];
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| | 34 | case 'spring green'
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| | 35 | homolog_a_color = [0.0 1.0 0.5];
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| | 36 | case 'green'
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| | 37 | homolog_a_color = [0.0 1.0 0.0];
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| | 38 | case 'chartreuse'
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| | 39 | homolog_a_color = [0.5 1.0 0.0];
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| | 40 | case 'yellow'
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| | 41 | homolog_a_color = [1.0 1.0 0.0];
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| | 42 | case 'dark orange'
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| | 43 | homolog_a_color = [1.0 0.5 0.0];
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| | 44 | case 'red'
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| | 45 | homolog_a_color = [1.0 0.0 0.0];
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| | 46 | end;
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| | 47 | switch colorB_string
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| | 48 | case 'deep pink'
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| | 49 | homolog_b_color = [1.0 0.0 0.5];
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| | 50 | case 'magenta'
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| | 51 | homolog_b_color = [1.0 0.0 1.0];
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| | 52 | case 'electric indigo'
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| | 53 | homolog_b_color = [0.5 0.0 1.0];
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| | 54 | case 'blue'
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| | 55 | homolog_b_color = [0.0 0.0 1.0];
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| | 56 | case 'dodger blue'
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| | 57 | homolog_b_color = [0.0 0.5 1.0];
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| | 58 | case 'cyan'
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| | 59 | homolog_b_color = [0.0 1.0 1.0];
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| | 60 | case 'spring green'
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| | 61 | homolog_b_color = [0.0 1.0 0.5];
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| | 62 | case 'green'
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| | 63 | homolog_b_color = [0.0 1.0 0.0];
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| | 64 | case 'chartreuse'
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| | 65 | homolog_b_color = [0.5 1.0 0.0];
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| | 66 | case 'yellow'
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| | 67 | homolog_b_color = [1.0 1.0 0.0];
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| | 68 | case 'dark orange'
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| | 69 | homolog_b_color = [1.0 0.5 0.0];
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| | 70 | case 'red'
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| | 71 | homolog_b_color = [1.0 0.0 0.0];
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| | 72 | end;
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| 1 | 73 | else
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| | 74 | % Haplotype map is not in use.
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| 1 | 75 | if (strcmp(project,hapmap) == 1)
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| | 76 | % The 'project' is the same as the 'hapmap'/'parent'.
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| | 77 | homolog_a_color = [0.66667 0.66667 0.66667];
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| | 78 | homolog_b_color = [0.66667 0.66667 0.66667];
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| 1 | 79 | else
|
| | 80 | % The 'project' is different than the 'hapmap'/'parent'.
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| 1 | 81 | homolog_a_color = [1.0 0.0 0.0];
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| 1 | 82 | homolog_b_color = [1.0 0.0 0.0];
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| 1 | 83 | end;
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| 1 | 84 | end;
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| 1 | 85 | hom_color = [1.0 0.0 0.0 ]; % completely homozygous.
|
| 1 | 86 | het_color = [0.66667 0.66667 0.66667]; % heterozygous.
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| 1 | 87 | oddHet_color = [0.0 1.0 0.0 ]; % non-heterozygous data that isn't 100 hom.
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| | 88 |
|
| | 89 |
|
| | 90 | %%%%%%%% phased data colors.
|
| | 91 |
|
| | 92 | % haploid colors.
|
| 1 | 93 | colorA = homolog_a_color;
|
| 1 | 94 | colorB = homolog_b_color;
|
| | 95 | % diploid colors.
|
| 1 | 96 | colorAA = homolog_a_color;
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| 1 | 97 | colorAB = het_color;
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| 1 | 98 | colorBB = homolog_b_color;
|
| | 99 | % triploid colors.
|
| 1 | 100 | colorAAA = homolog_a_color;
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| 1 | 101 | colorAAB = homolog_a_color*2/3 + homolog_b_color*1/3;
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| 1 | 102 | colorABB = homolog_a_color*1/3 + homolog_b_color*2/3;
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| 1 | 103 | colorBBB = homolog_b_color;
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| | 104 | % tetraploid colors.
|
| 1 | 105 | colorAAAA = homolog_a_color;
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| 1 | 106 | colorAAAB = homolog_a_color*3/4 + homolog_b_color*1/4;
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| 1 | 107 | colorAABB = het_color;
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| 1 | 108 | colorABBB = homolog_a_color*1/4 + homolog_b_color*3/4;
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| 1 | 109 | colorBBBB = homolog_b_color;
|
| | 110 | % pentaploid colors.
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| 1 | 111 | colorAAAAA = homolog_a_color;
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| 1 | 112 | colorAAAAB = homolog_a_color*4/5 + homolog_b_color*1/5;
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| 1 | 113 | colorAAABB = homolog_a_color*3/5 + homolog_b_color*2/5;
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| 1 | 114 | colorAABBB = homolog_a_color*2/5 + homolog_b_color*3/5;
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| 1 | 115 | colorABBBB = homolog_a_color*1/5 + homolog_b_color*4/5;
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| 1 | 116 | colorBBBBB = homolog_b_color;
|
| | 117 | % hexaploid colors.
|
| 1 | 118 | colorAAAAAA = homolog_a_color;
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| 1 | 119 | colorAAAAAB = homolog_a_color*5/6 + homolog_b_color*1/6;
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| 1 | 120 | colorAAAABB = homolog_a_color*4/6 + homolog_b_color*2/6;
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| 1 | 121 | colorAAABBB = het_color;
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| 1 | 122 | colorAABBBB = homolog_a_color*2/6 + homolog_b_color*4/6;
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| 1 | 123 | colorABBBBB = homolog_a_color*1/6 + homolog_b_color*5/6;
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| 1 | 124 | colorBBBBBB = homolog_b_color;
|
| | 125 | % heptaploid colors.
|
| 1 | 126 | colorAAAAAAA = homolog_a_color;
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| 1 | 127 | colorAAAAAAB = homolog_a_color*6/7 + homolog_b_color*1/7;
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| 1 | 128 | colorAAAAABB = homolog_a_color*5/7 + homolog_b_color*2/7;
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| 1 | 129 | colorAAAABBB = homolog_a_color*4/7 + homolog_b_color*3/7;
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| 1 | 130 | colorAAABBBB = homolog_a_color*3/7 + homolog_b_color*4/7;
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| 1 | 131 | colorAABBBBB = homolog_a_color*2/7 + homolog_b_color*5/7;
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| 1 | 132 | colorABBBBBB = homolog_a_color*1/7 + homolog_b_color*6/7;
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| 1 | 133 | colorBBBBBBB = homolog_b_color;
|
| | 134 | % octaploid colors.
|
| 1 | 135 | colorAAAAAAAA = homolog_a_color;
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| 1 | 136 | colorAAAAAAAB = homolog_a_color*7/8 + homolog_b_color*1/8;
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| 1 | 137 | colorAAAAAABB = homolog_a_color*6/8 + homolog_b_color*2/8;
|
| 1 | 138 | colorAAAAABBB = homolog_a_color*5/8 + homolog_b_color*3/8;
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| 1 | 139 | colorAAAABBBB = het_color;
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| 1 | 140 | colorAAABBBBB = homolog_a_color*3/8 + homolog_b_color*5/8;
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| 1 | 141 | colorAABBBBBB = homolog_a_color*2/8 + homolog_b_color*6/8;
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| 1 | 142 | colorABBBBBBB = homolog_a_color*1/8 + homolog_b_color*7/8;
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| 1 | 143 | colorBBBBBBBB = homolog_b_color;
|
| | 144 | % nonaploid colors.
|
| 1 | 145 | colorAAAAAAAAA = homolog_a_color;
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| 1 | 146 | colorAAAAAAAAB = homolog_a_color*8/9 + homolog_b_color*1/9;
|
| 1 | 147 | colorAAAAAAABB = homolog_a_color*7/9 + homolog_b_color*2/9;
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| 1 | 148 | colorAAAAAABBB = homolog_a_color*6/9 + homolog_b_color*3/9;
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| 1 | 149 | colorAAAAABBBB = homolog_a_color*5/9 + homolog_b_color*4/9;
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| 1 | 150 | colorAAAABBBBB = homolog_a_color*4/9 + homolog_b_color*5/9;
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| 1 | 151 | colorAAABBBBBB = homolog_a_color*3/9 + homolog_b_color*6/9;
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| 1 | 152 | colorAABBBBBBB = homolog_a_color*2/9 + homolog_b_color*7/9;
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| 1 | 153 | colorABBBBBBBB = homolog_a_color*1/9 + homolog_b_color*8/9;
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| 1 | 154 | colorBBBBBBBBB = homolog_b_color;
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| | 155 |
|
| | 156 |
|
| | 157 | %%%%%%%% unphased colors.
|
| | 158 |
|
| | 159 | % haploid colors.
|
| 1 | 160 | unphased_color_1of1 = hom_color;
|
| | 161 | % diploid colors.
|
| 1 | 162 | unphased_color_2of2 = hom_color;
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| 1 | 163 | unphased_color_1of2 = het_color;
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| | 164 | % triploid colors.
|
| 1 | 165 | unphased_color_3of3 = hom_color;
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| 1 | 166 | unphased_color_2of3 = hom_color*1/3 + het_color*2/3;
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| | 167 | % tetraploid colors.
|
| 1 | 168 | unphased_color_4of4 = hom_color;
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| 1 | 169 | unphased_color_3of4 = hom_color*1/2 + het_color*1/2;
|
| 1 | 170 | unphased_color_2of4 = het_color;
|
| | 171 | % pentaploid colors.
|
| 1 | 172 | unphased_color_5of5 = hom_color;
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| 1 | 173 | unphased_color_4of5 = hom_color*3/5 + het_color*2/5;
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| 1 | 174 | unphased_color_3of5 = hom_color*1/5 + het_color*4/5;
|
| | 175 | % hexaploid colors.
|
| 1 | 176 | unphased_color_6of6 = hom_color;
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| 1 | 177 | unphased_color_5of6 = hom_color*4/6 + het_color*2/6;
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| 1 | 178 | unphased_color_4of6 = hom_color*2/6 + het_color*4/6;
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| 1 | 179 | unphased_color_3of6 = het_color;
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| | 180 | % heptaploid colors.
|
| 1 | 181 | unphased_color_7of7 = hom_color;
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| 1 | 182 | unphased_color_6of7 = hom_color*5/7 + het_color*2/7;
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| 1 | 183 | unphased_color_5of7 = hom_color*3/7 + het_color*4/7;
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| 1 | 184 | unphased_color_4of7 = hom_color*1/7 + het_color*6/7;
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| | 185 | % octaploid colors.
|
| 1 | 186 | unphased_color_8of8 = hom_color;
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| 1 | 187 | unphased_color_7of8 = hom_color*6/8 + het_color*2/8;
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| 1 | 188 | unphased_color_6of8 = hom_color*4/8 + het_color*4/8;
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| 1 | 189 | unphased_color_5of8 = hom_color*2/8 + het_color*6/8;
|
| 1 | 190 | unphased_color_4of8 = het_color;
|
| | 191 | % nonaploid colors.
|
| 1 | 192 | unphased_color_9of9 = hom_color;
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| 1 | 193 | unphased_color_8of9 = hom_color*7/9 + het_color*2/9;
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| 1 | 194 | unphased_color_7of9 = hom_color*5/9 + het_color*4/9;
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| 1 | 195 | unphased_color_6of9 = hom_color*3/9 + het_color*6/9;
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| 1 | 196 | unphased_color_5of9 = hom_color*1/9 + het_color*8/9;
|
| | 197 |
|
| | 198 |
|
| | 199 | %%%%%%%% colors for no parent.
|
| | 200 |
|
| | 201 | % haploid colors.
|
| 1 | 202 | noparent_color_1of1 = colorNoData;
|
| | 203 | % diploid colors.
|
| 1 | 204 | noparent_color_2of2 = colorNoData;
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| 1 | 205 | noparent_color_1of2 = het_color;
|
| | 206 | % triploid colors.
|
| 1 | 207 | noparent_color_3of3 = colorNoData;
|
| 1 | 208 | noparent_color_2of3 = colorNoData*1/3 + het_color*2/3;
|
| | 209 | % tetraploid colors.
|
| 1 | 210 | noparent_color_4of4 = colorNoData;
|
| 1 | 211 | noparent_color_3of4 = colorNoData*1/2 + het_color*1/2;
|
| 1 | 212 | noparent_color_2of4 = het_color;
|
| | 213 | % pentaploid colors.
|
| 1 | 214 | noparent_color_5of5 = colorNoData;
|
| 1 | 215 | noparent_color_4of5 = colorNoData*3/5 + het_color*2/5;
|
| 1 | 216 | noparent_color_3of5 = colorNoData*1/5 + het_color*4/5;
|
| | 217 | % hexaploid colors.
|
| 1 | 218 | noparent_color_6of6 = colorNoData;
|
| 1 | 219 | noparent_color_5of6 = colorNoData*4/6 + het_color*2/6;
|
| 1 | 220 | noparent_color_4of6 = colorNoData*2/6 + het_color*4/6;
|
| 1 | 221 | noparent_color_3of6 = het_color;
|
| | 222 | % heptaploid colors.
|
| 1 | 223 | noparent_color_7of7 = colorNoData;
|
| 1 | 224 | noparent_color_6of7 = colorNoData*5/7 + het_color*2/7;
|
| 1 | 225 | noparent_color_5of7 = colorNoData*3/7 + het_color*4/7;
|
| 1 | 226 | noparent_color_4of7 = colorNoData*1/7 + het_color*6/7;
|
| | 227 | % octaploid colors.
|
| 1 | 228 | noparent_color_8of8 = colorNoData;
|
| 1 | 229 | noparent_color_7of8 = colorNoData*6/8 + het_color*2/8;
|
| 1 | 230 | noparent_color_6of8 = colorNoData*4/8 + het_color*4/8;
|
| 1 | 231 | noparent_color_5of8 = colorNoData*2/8 + het_color*6/8;
|
| 1 | 232 | noparent_color_4of8 = het_color;
|
| | 233 | % nonaploid colors.
|
| 1 | 234 | noparent_color_9of9 = colorNoData;
|
| 1 | 235 | noparent_color_8of9 = colorNoData*7/9 + het_color*2/9;
|
| 1 | 236 | noparent_color_7of9 = colorNoData*5/9 + het_color*4/9;
|
| 1 | 237 | noparent_color_6of9 = colorNoData*3/9 + het_color*6/9;
|
| 1 | 238 | noparent_color_5of9 = colorNoData*1/9 + het_color*8/9;
|
| | 239 |
|
| | 240 |
|
| | 241 | %%%%%%%% alternate colors for use with hapmap or parent.
|
| | 242 |
|
| | 243 | % haploid colors.
|
| 1 | 244 | alternate_color_1of1 = hom_color;
|
| | 245 | % diploid colors.
|
| 1 | 246 | alternate_color_2of2 = hom_color;
|
| 1 | 247 | alternate_color_1of2 = het_color;
|
| | 248 | % triploid colors.
|
| 1 | 249 | alternate_color_3of3 = hom_color;
|
| 1 | 250 | alternate_color_2of3 = oddHet_color;
|
| | 251 | % tetraploid colors.
|
| 1 | 252 | alternate_color_4of4 = hom_color
|
| 1 | 253 | alternate_color_3of4 = oddHet_color;
|
| 1 | 254 | alternate_color_2of4 = het_color;
|
| | 255 | % pentaploid colors.
|
| 1 | 256 | alternate_color_5of5 = hom_color;
|
| 1 | 257 | alternate_color_4of5 = oddHet_color;
|
| 1 | 258 | alternate_color_3of5 = oddHet_color;
|
| | 259 | % hexaploid colors.
|
| 1 | 260 | alternate_color_6of6 = hom_color;
|
| 1 | 261 | alternate_color_5of6 = oddHet_color;
|
| 1 | 262 | alternate_color_4of6 = oddHet_color;
|
| 1 | 263 | alternate_color_3of6 = het_color;
|
| | 264 | % heptaploid colors.
|
| 1 | 265 | alternate_color_7of7 = hom_color;
|
| 1 | 266 | alternate_color_6of7 = oddHet_color;
|
| 1 | 267 | alternate_color_5of7 = oddHet_color;
|
| 1 | 268 | alternate_color_4of7 = oddHet_color;
|
| | 269 | % octaploid colors.
|
| 1 | 270 | alternate_color_8of8 = hom_color;
|
| 1 | 271 | alternate_color_7of8 = oddHet_color;
|
| 1 | 272 | alternate_color_6of8 = oddHet_color;
|
| 1 | 273 | alternate_color_5of8 = oddHet_color;
|
| 1 | 274 | alternate_color_4of8 = het_color;
|
| | 275 | % nonaploid colors.
|
| 1 | 276 | alternate_color_9of9 = hom_color;
|
| 1 | 277 | alternate_color_8of9 = oddHet_color;
|
| 1 | 278 | alternate_color_7of9 = oddHet_color;
|
| 1 | 279 | alternate_color_6of9 = oddHet_color;
|
| 1 | 280 | alternate_color_5of9 = oddHet_color;
|