From 515662ecabd5d3a90eef6987aa5f8d4dbe63611f Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Mon, 19 May 2014 22:03:31 +0000 Subject: Fixed sorting on the show trait page Added/improved the x and y axis on the bar graph and histogram GEMMA working but still really slow --- web/gemma/output/HLC_output.assoc.txt | 546698 +++++++++--------- web/gemma/output/HLC_output.log.txt | 22 +- .../wqflask/marker_regression/marker_regression.py | 6 + wqflask/wqflask/show_trait/show_trait.py | 5 +- wqflask/wqflask/static/new/css/bar_chart.css | 4 +- .../wqflask/static/new/javascript/histogram.coffee | 38 +- wqflask/wqflask/static/new/javascript/histogram.js | 16 +- .../static/new/javascript/show_trait.coffee | 1 + .../new/javascript/show_trait_mapping_tools.coffee | 35 + .../new/javascript/show_trait_mapping_tools.js | 36 + wqflask/wqflask/templates/show_trait.html | 126 +- .../templates/show_trait_mapping_tools.html | 65 +- 12 files changed, 273630 insertions(+), 273422 deletions(-) diff --git a/web/gemma/output/HLC_output.assoc.txt b/web/gemma/output/HLC_output.assoc.txt index 066b2e6d..d10b9137 100644 --- a/web/gemma/output/HLC_output.assoc.txt +++ b/web/gemma/output/HLC_output.assoc.txt @@ -1,273350 +1,273350 @@ chr rs ps n_miss allele1 allele0 af beta se l_remle p_wald -0 rs1155740 0 18 T C 0.274 3.657362e+01 2.959468e+01 1.474382e+01 2.172090e-01 -0 rs1169469 0 16 T C 0.105 1.051056e+01 4.306356e+01 1.484068e+01 8.072938e-01 -0 rs11775 0 19 G A 0.327 -3.713332e+01 2.802305e+01 1.327030e+01 1.858502e-01 -0 rs1368258 0 13 T C 0.343 4.317085e+01 2.884774e+01 1.515606e+01 1.352637e-01 -0 rs1414747 0 17 A C 0.446 7.444262e+00 2.577342e+01 1.474551e+01 7.728486e-01 -0 rs1459037 0 7 G A 0.290 -8.095321e+00 2.877323e+01 1.467617e+01 7.785796e-01 -0 rs150775 0 20 T G 0.061 -4.064932e+00 5.527824e+01 1.486203e+01 9.414143e-01 -0 rs1538704 0 6 G A 0.292 -1.015838e+01 2.739498e+01 1.471320e+01 7.109626e-01 -0 rs1578301 0 0 C T 0.447 1.596911e+01 2.657632e+01 1.482601e+01 5.482419e-01 -0 rs16907085 0 1 G A 0.124 4.403192e+01 4.017091e+01 1.468063e+01 2.736494e-01 -0 rs16992891 0 3 T C 0.333 9.826730e-02 2.708139e+01 1.483524e+01 9.971065e-01 -0 rs17566573 0 20 A G 0.195 3.087860e+01 3.361346e+01 1.478049e+01 3.588060e-01 -0 rs2229935 0 1 T C 0.275 -2.691205e+01 2.919483e+01 1.498852e+01 3.571513e-01 -0 rs2230394 0 5 T C 0.098 1.171663e+01 4.486701e+01 1.489657e+01 7.941100e-01 -0 rs2230395 0 1 C A 0.101 2.252935e+01 4.418118e+01 1.493292e+01 6.103646e-01 -0 rs2387949 0 8 A G 0.119 1.815905e+01 3.850873e+01 1.478549e+01 6.374853e-01 -0 rs2565615 0 21 T A 0.498 -1.543149e+00 2.721993e+01 1.480421e+01 9.548173e-01 -0 rs2886026 0 5 G A 0.435 -1.149330e+01 2.657613e+01 1.492739e+01 6.656212e-01 -0 rs2886027 0 18 A G 0.436 -4.772916e+00 2.702424e+01 1.487982e+01 8.598941e-01 -0 rs2903177 0 11 G A 0.050 -3.740485e+01 5.665480e+01 1.380411e+01 5.094678e-01 -0 rs2903407 0 1 G A 0.130 8.295727e+01 3.856454e+01 1.454574e+01 3.202913e-02 -0 rs3818890 0 7 A G 0.044 -1.060077e+02 6.369006e+01 1.508185e+01 9.676343e-02 -0 rs3885710 0 2 C T 0.029 6.908315e+01 7.476742e+01 1.490523e+01 3.560241e-01 -0 rs3923989 0 3 G A 0.208 1.425102e+01 3.165766e+01 1.501490e+01 6.528245e-01 -0 rs3928422 0 15 T C 0.476 7.669558e+00 2.578491e+01 1.496195e+01 7.662732e-01 -0 rs3929758 0 0 C A 0.276 6.095513e+00 2.862785e+01 1.482282e+01 8.314895e-01 -0 rs3963196 0 6 C G 0.110 -4.132618e+01 4.205020e+01 1.458302e+01 3.262739e-01 -0 rs3990898 0 19 T C 0.475 1.210375e+01 2.665857e+01 1.482063e+01 6.500400e-01 -0 rs4000844 0 3 C T 0.324 1.305142e+01 2.718158e+01 1.482681e+01 6.313630e-01 -0 rs449837 0 2 C T 0.120 -1.854300e+01 3.883986e+01 1.482784e+01 6.333072e-01 -0 rs5749531 0 6 C T 0.270 -1.860765e+01 2.882072e+01 1.438566e+01 5.188645e-01 -0 rs828748 0 13 A T 0.469 -8.225675e+00 2.509246e+01 1.490868e+01 7.432132e-01 -0 rs9620258 0 18 T C 0.465 3.346972e+01 2.711623e+01 1.491335e+01 2.177710e-01 -0 rs9625253 0 2 C G 0.166 5.663989e+01 3.361768e+01 1.453813e+01 9.275658e-02 -1 rs4040617 819184 0 G A 0.129 -6.893390e+01 3.809609e+01 1.475634e+01 7.108365e-02 -1 rs4075116 1043551 3 G A 0.303 1.647354e+01 2.721051e+01 1.495971e+01 5.452292e-01 -1 rs10907175 1170649 2 C A 0.104 -6.110439e-01 4.170067e+01 1.483898e+01 9.883158e-01 -1 rs6603781 1198553 9 A G 0.104 5.062098e+01 4.514516e+01 1.491001e+01 2.627961e-01 -1 rs6685064 1251214 1 T C 0.072 -2.780089e+01 4.939713e+01 1.482850e+01 5.738653e-01 -1 rs1695824 1450836 7 G T 0.242 5.386828e+01 3.030474e+01 1.476389e+01 7.619232e-02 -1 rs3766180 1563419 10 G A 0.294 2.897535e+00 2.731324e+01 1.485556e+01 9.155647e-01 -1 rs6603791 1586207 5 G A 0.315 -3.440587e-01 2.721297e+01 1.484617e+01 9.899184e-01 -1 rs2281173 1720353 8 A G 0.094 1.495779e+01 4.303851e+01 1.478164e+01 7.283545e-01 -1 rs1107910 1724482 11 G A 0.444 2.743260e+01 2.546984e+01 1.464517e+01 2.820636e-01 -1 rs2272908 1753640 6 T C 0.499 -3.980223e+01 2.403059e+01 1.462926e+01 9.839611e-02 -1 rs3737628 1755093 7 T C 0.496 -3.717349e+01 2.446433e+01 1.457457e+01 1.293809e-01 -1 rs9786963 1791187 11 T C 0.055 2.042592e+01 5.400283e+01 1.477781e+01 7.054426e-01 -1 rs10907187 1791215 2 A G 0.280 -5.016003e+00 2.826126e+01 1.485985e+01 8.592105e-01 -1 rs7511905 1825947 1 A C 0.055 1.382402e+01 5.349213e+01 1.479337e+01 7.961995e-01 -1 rs6603803 1844849 1 G A 0.496 -4.681854e+01 2.412199e+01 1.455499e+01 5.293041e-02 -1 rs6688000 1856083 17 A G 0.057 1.553305e+01 5.364052e+01 1.478819e+01 7.722813e-01 -1 rs2803285 1920530 13 T C 0.164 1.305349e+01 3.498821e+01 1.497425e+01 7.092730e-01 -1 rs7513222 2060062 4 A G 0.342 5.648919e+01 2.510735e+01 1.448039e+01 2.496577e-02 -1 rs3107146 2079745 10 T C 0.118 3.788530e+00 3.943622e+01 1.484030e+01 9.235124e-01 -1 rs385039 2109570 8 G A 0.289 9.726101e+00 2.746887e+01 1.483417e+01 7.234567e-01 -1 rs3128309 2138039 13 A G 0.091 -8.921794e+01 4.406916e+01 1.390363e+01 4.354380e-02 -1 rs262680 2199310 21 A G 0.413 2.909231e+00 2.677121e+01 1.481841e+01 9.135154e-01 -1 rs16824948 2218381 6 T C 0.056 -6.635991e+01 5.693121e+01 1.466248e+01 2.444236e-01 -1 rs12084736 2221741 2 T C 0.061 6.665888e+01 5.419359e+01 1.463453e+01 2.193723e-01 -1 rs2132303 2255419 2 T C 0.135 5.126253e+01 3.669327e+01 1.450071e+01 1.631259e-01 -1 rs1496555 2266412 1 A G 0.133 5.057820e+01 3.617845e+01 1.452568e+01 1.628362e-01 -1 rs7527871 2313887 15 C A 0.161 -9.560611e+00 3.388601e+01 1.485690e+01 7.779732e-01 -1 rs2843130 2315474 3 C G 0.171 3.204022e+01 3.293102e+01 1.494647e+01 3.311318e-01 -1 rs2840528 2316057 3 G A 0.434 1.209219e+01 2.603078e+01 1.480055e+01 6.425027e-01 -1 rs7545940 2331788 1 C T 0.344 -4.040628e+01 2.780182e+01 1.468452e+01 1.468594e-01 -1 rs10910060 2335072 10 A G 0.223 3.874450e+01 3.091159e+01 1.466587e+01 2.107502e-01 -1 rs4648633 2352863 4 C T 0.232 -4.779012e+01 3.083863e+01 1.487421e+01 1.219618e-01 -1 rs12023660 2389971 11 T C 0.102 3.449007e+01 4.279978e+01 1.484861e+01 4.207818e-01 -1 rs7512269 2450786 7 T C 0.124 -8.923525e+00 3.994253e+01 1.488074e+01 8.233244e-01 -1 rs2246732 2482555 4 C T 0.228 2.027621e+01 3.185534e+01 1.481628e+01 5.247874e-01 -1 rs2985862 2484730 6 A G 0.236 -2.511441e+01 3.059901e+01 1.461329e+01 4.122437e-01 -1 rs3122922 2488364 1 T C 0.201 -2.268773e+01 3.192467e+01 1.470526e+01 4.776820e-01 -1 rs10910093 2537874 1 T C 0.129 -2.610509e+01 3.954803e+01 1.476189e+01 5.095565e-01 -1 rs4486391 2545216 3 T A 0.483 -9.088419e+00 2.701707e+01 1.492888e+01 7.367387e-01 -1 rs10910097 2553591 11 T C 0.192 -2.731993e+01 3.296366e+01 1.461338e+01 4.076888e-01 -1 rs6684865 2578390 14 A G 0.328 2.846684e+01 2.768102e+01 1.452968e+01 3.043522e-01 -1 rs3890745 2585785 3 G A 0.323 2.892865e+01 2.756848e+01 1.446371e+01 2.946189e-01 -1 rs2377041 2736484 16 A G 0.438 4.161363e+00 2.716628e+01 1.484215e+01 8.783281e-01 -1 rs4648360 2746501 15 T C 0.453 -9.514698e+00 2.721073e+01 1.481233e+01 7.267617e-01 -1 rs729045 2777562 21 C T 0.451 1.517097e+01 2.678594e+01 1.481178e+01 5.714357e-01 -1 rs6680471 2777668 1 T C 0.471 -3.980224e+00 2.732303e+01 1.485243e+01 8.842487e-01 -1 rs12049543 2784531 7 A C 0.448 -6.511709e+00 2.582748e+01 1.484826e+01 8.010676e-01 -1 rs897631 2848523 0 C T 0.248 -4.603106e+01 3.053936e+01 1.483860e+01 1.324844e-01 -1 rs897632 2849319 15 A G 0.257 -3.484784e+01 3.080992e+01 1.487995e+01 2.586681e-01 -1 rs10752728 2867410 18 T A 0.244 -2.795404e+01 3.170386e+01 1.490226e+01 3.784246e-01 -1 rs897635 2869430 13 T A 0.245 -1.342239e+01 3.129354e+01 1.487976e+01 6.681996e-01 -1 rs1869972 2874394 14 A G 0.324 -1.734814e+01 2.846867e+01 1.392952e+01 5.426004e-01 -1 rs2606414 2890304 7 T C 0.301 1.704726e+01 2.898365e+01 1.477040e+01 5.567318e-01 -1 rs6659552 2902616 8 C G 0.245 -1.705238e+00 2.990699e+01 1.485462e+01 9.545576e-01 -1 rs10909855 2931544 4 T C 0.128 1.973449e+01 4.083656e+01 1.474449e+01 6.291632e-01 -1 rs17391750 2932527 12 A G 0.112 1.162354e+01 4.421929e+01 1.478237e+01 7.927849e-01 -1 rs6661908 2973490 2 A G 0.189 2.115759e+01 3.474291e+01 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-1 rs2493310 3317578 2 C T 0.161 3.258402e+01 3.493227e+01 1.483291e+01 3.514648e-01 -1 rs2493275 3331190 2 T C 0.102 -2.877670e+01 4.243265e+01 1.473134e+01 4.980308e-01 -1 rs17822581 3337752 14 G A 0.191 -2.091173e+01 3.366542e+01 1.484760e+01 5.348251e-01 -1 rs17400178 3363391 6 T G 0.055 -2.577906e+01 5.901805e+01 1.476976e+01 6.624785e-01 -1 rs2487681 3400499 4 G A 0.142 4.066042e+01 3.626015e+01 1.512881e+01 2.627709e-01 -1 rs2821041 3427383 4 A G 0.151 2.550232e+01 3.579602e+01 1.501450e+01 4.765868e-01 -1 rs4648505 3428452 3 C T 0.177 6.640686e+00 3.361946e+01 1.488504e+01 8.435111e-01 -1 rs10909969 3503305 10 T C 0.276 5.310876e+01 2.765667e+01 1.456852e+01 5.549054e-02 -1 rs17379833 3643336 1 T A 0.393 -1.135327e+01 2.656775e+01 1.496571e+01 6.693535e-01 -1 rs6424090 3651833 4 A G 0.046 -1.945625e+01 6.022430e+01 1.480011e+01 7.468063e-01 -1 rs12120656 3689023 5 T G 0.350 -3.015145e+01 2.640386e+01 1.463415e+01 2.541246e-01 -1 rs1181889 3694183 7 G A 0.117 -2.782612e+01 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-5.536532e+02 4.692019e+02 1.433380e+00 2.386645e-01 +23 rs7882041 150779636 8 G T 0.150 -7.194876e+01 4.108680e+02 1.397490e+00 8.610734e-01 +23 rs5970169 150782245 17 T G 0.128 -1.036587e+02 4.544776e+02 1.390441e+00 8.196913e-01 +23 rs12011671 150795532 7 C T 0.327 -4.439811e+02 3.141186e+02 9.928050e-01 1.582647e-01 +23 rs2157012 150833514 6 G C 0.223 2.578414e+02 3.539034e+02 1.490998e+00 4.666693e-01 +23 rs11094534 150853849 4 T C 0.215 2.724552e+02 3.573909e+02 1.481916e+00 4.462770e-01 +23 rs5970194 150911182 10 A G 0.210 3.397690e+02 3.642925e+02 1.511995e+00 3.515139e-01 +23 rs1844894 150932710 11 G A 0.130 1.070672e+03 4.440570e+02 1.112049e+00 1.632718e-02 +23 rs210584 150975511 21 G A 0.339 4.812532e+02 3.076351e+02 9.458664e-01 1.184764e-01 +23 rs1491793 151004671 14 A T 0.249 1.503103e+02 3.378194e+02 1.255171e+00 6.565877e-01 +23 rs994424 151052347 8 C T 0.161 -1.709513e+02 4.014392e+02 1.502567e+00 6.704356e-01 +23 rs7064104 151062197 5 G A 0.168 -6.079142e+01 3.914561e+02 1.441200e+00 8.766620e-01 +23 3884087 151116918 12 C T 0.090 2.909932e+01 4.907204e+02 1.408545e+00 9.527417e-01 +23 rs5925155 151128485 7 G A 0.339 -3.563930e+01 3.046420e+02 1.462880e+00 9.069252e-01 +23 rs4828696 151252563 16 T C 0.384 7.347406e+02 3.044403e+02 1.605889e+00 1.622594e-02 +23 rs6627595 151288570 10 C G 0.415 2.645035e+02 3.009935e+02 1.462225e+00 3.800237e-01 +23 rs6627611 151439733 8 G A 0.329 2.497407e+02 3.152583e+02 1.472238e+00 4.286987e-01 +23 rs5924753 151488575 8 C T 0.470 -5.243616e+02 2.961691e+02 1.471323e+00 7.736392e-02 +23 rs2471773 151569922 5 T C 0.444 5.310596e+02 2.964658e+02 1.252075e+00 7.395639e-02 +23 rs2515832 151572621 2 C G 0.446 5.165314e+02 2.948847e+02 1.195249e+00 8.055724e-02 +23 rs6526129 151652671 1 A G 0.089 3.776517e+00 5.055515e+02 1.402930e+00 9.940433e-01 +23 rs3088344 151666353 7 T G 0.120 -2.438402e+02 4.709570e+02 1.294921e+00 6.048989e-01 +23 rs6627690 151672683 4 A T 0.040 1.342831e+02 7.476757e+02 1.365165e+00 8.575516e-01 +23 rs12845949 151688319 21 A G 0.284 -1.011003e+02 3.268018e+02 1.334796e+00 7.571972e-01 +23 rs5970391 151712954 6 T G 0.493 1.669590e+02 2.918648e+02 1.256621e+00 5.675959e-01 +23 rs6526138 151718162 20 A G 0.299 1.121662e+02 3.284373e+02 1.402478e+00 7.328849e-01 +23 rs5925239 151729952 2 C T 0.213 1.750042e+02 3.487526e+02 1.398059e+00 6.160677e-01 +23 rs5969921 151731439 20 C T 0.134 -8.675578e+00 4.624357e+02 1.402951e+00 9.850409e-01 +23 rs2071257 151759270 3 G T 0.204 -1.875519e+02 3.604521e+02 1.378771e+00 6.031086e-01 +23 rs10126824 151778651 8 T C 0.085 -4.540913e+02 5.384163e+02 1.337699e+00 3.994885e-01 +23 rs5925268 151808635 21 T C 0.267 -1.992814e+02 3.316334e+02 1.311576e+00 5.482212e-01 +23 rs12560037 151839176 19 T C 0.331 -3.782045e+02 3.092107e+02 1.408205e+00 2.219588e-01 +23 rs2382883 151873256 3 A G 0.065 5.332619e+02 5.749897e+02 1.010210e+00 3.542305e-01 +23 rs6627738 151900925 14 C T 0.059 5.159894e+02 6.112936e+02 1.099143e+00 3.990916e-01 +23 rs4828744 151925407 4 G A 0.070 6.633532e+02 5.537957e+02 8.364750e-01 2.316507e-01 +23 rs4828747 151929154 8 C T 0.074 8.191338e+02 5.461813e+02 6.878073e-01 1.344224e-01 +23 rs2008144 151966996 4 A G 0.069 6.653272e+02 5.622074e+02 8.150273e-01 2.373045e-01 +23 rs5925336 151987489 20 T C 0.189 5.057982e+02 3.782736e+02 1.091805e+00 1.818978e-01 +23 rs1894342 151987996 11 G A 0.066 7.920495e+02 5.760390e+02 7.318519e-01 1.698581e-01 +23 rs1557505 151992064 2 G A 0.181 4.906312e+02 3.758148e+02 1.107522e+00 1.924245e-01 +23 rs5924813 151995603 7 C T 0.060 1.050542e+03 6.060025e+02 5.676362e-01 8.372142e-02 +23 rs2012435 152010745 2 T C 0.068 7.649911e+02 5.614145e+02 7.160548e-01 1.737259e-01 +23 rs2012436 152010777 2 G C 0.068 7.649911e+02 5.614145e+02 7.160548e-01 1.737259e-01 +23 rs5925368 152033116 13 G A 0.056 4.850721e+02 6.443881e+02 1.060616e+00 4.520085e-01 +23 rs6627772 152053967 5 A G 0.327 -7.348535e+02 3.037732e+02 1.913365e+00 1.597861e-02 +23 rs995423 152085362 13 A T 0.488 -2.302553e+01 2.949064e+02 1.418232e+00 9.378032e-01 +23 rs1894354 152089815 0 T C 0.177 -8.651713e+01 3.852254e+02 1.493356e+00 8.224075e-01 +23 rs5986911 152351829 6 T A 0.036 -6.052153e+02 8.346069e+02 1.458641e+00 4.687590e-01 +23 rs5945145 152351894 5 C T 0.405 2.556045e+00 2.973697e+02 1.405507e+00 9.931459e-01 +23 rs4898424 152360329 16 G T 0.274 8.014956e+01 3.346344e+02 1.358128e+00 8.108226e-01 +23 rs4898428 152397543 12 A G 0.134 -5.622230e+02 4.425575e+02 1.452369e+00 2.046388e-01 +23 rs3761536 152427138 16 A T 0.178 -2.451683e+02 3.896597e+02 1.624546e+00 5.295654e-01 +23 rs5987140 152521101 20 C T 0.111 3.357028e+01 4.930577e+02 1.405850e+00 9.457493e-01 +23 rs2266887 152760433 8 T G 0.203 4.527955e+02 3.696201e+02 1.055914e+00 2.212426e-01 +23 rs7884370 152843727 5 G A 0.041 6.650459e+02 7.275102e+02 1.254241e+00 3.611618e-01 +23 rs1734791 152851766 13 T A 0.158 1.818275e+01 4.075201e+02 1.393589e+00 9.644327e-01 +23 rs766420 153075250 6 C G 0.220 -1.161442e+02 3.563688e+02 1.374410e+00 7.446527e-01 +23 rs766419 153075507 6 C T 0.219 -2.020163e+02 3.563200e+02 1.364275e+00 5.710461e-01 +23 rs2239467 153076140 14 G A 0.224 -1.279868e+02 3.576258e+02 1.367731e+00 7.206114e-01 +23 rs4898494 153174968 5 T A 0.108 4.589111e+02 4.725147e+02 1.486027e+00 3.319961e-01 +23 rs4898348 153450097 18 T C 0.231 1.085220e+03 3.552855e+02 1.654826e+00 2.396195e-03 +23 rs5945109 153471452 8 G A 0.377 5.977579e+02 3.064267e+02 1.532848e+00 5.174515e-02 +23 rs5945122 153737610 8 C A 0.135 3.680298e+01 4.337705e+02 1.429719e+00 9.324251e-01 +23 rs2051161 153849554 3 G C 0.383 7.052883e+02 3.026393e+02 1.477207e+00 2.024911e-02 +23 3885427 154017791 18 G A 0.232 -2.548193e+02 3.451999e+02 1.424038e+00 4.608131e-01 +23 rs475025 154048640 3 G A 0.243 -2.337655e+02 3.345153e+02 1.458479e+00 4.850476e-01 +23 rs6420603 154316683 14 G A 0.029 -1.355348e+02 8.962687e+02 1.416665e+00 8.798730e-01 +23 rs574386 154411192 9 C T 0.240 -3.510010e+02 3.367436e+02 1.408866e+00 2.978471e-01 diff --git a/web/gemma/output/HLC_output.log.txt b/web/gemma/output/HLC_output.log.txt index 9dd3d75b..e8107112 100644 --- a/web/gemma/output/HLC_output.log.txt +++ b/web/gemma/output/HLC_output.log.txt @@ -10,19 +10,19 @@ ## number of phenotypes = 1 ## number of total SNPs = 358499 ## number of analyzed SNPs = 273349 -## REMLE log-likelihood in the null model = -3121.45 -## MLE log-likelihood in the null model = -3127.35 -## pve estimate in the null model = 0.830303 -## se(pve) in the null model = 0.108674 -## vg estimate in the null model = 347865 -## ve estimate in the null model = 23515.2 -## beta estimate in the null model = 454.076 -## se(beta) = 7.42097 +## REMLE log-likelihood in the null model = -4252.51 +## MLE log-likelihood in the null model = -4261.76 +## pve estimate in the null model = 0.314624 +## se(pve) in the null model = 0.403683 +## vg estimate in the null model = 2.61389e+07 +## ve estimate in the null model = 1.88332e+07 +## beta estimate in the null model = 5107.48 +## se(beta) = 210.014 ## ## Computation Time: -## total computation time = 2.67 min +## total computation time = 2.5965 min ## computation time break down: ## time on eigen-decomposition = 0.0015 min -## time on calculating UtX = 0.4125 min -## time on optimization = 2.10517 min +## time on calculating UtX = 0.414167 min +## time on optimization = 2.03267 min ## diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 54cc9006..c220d2c9 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -58,6 +58,8 @@ class MarkerRegression(object): if self.mapping_method == "gemma": qtl_results = self.run_gemma() + elif self.mapping_method == "plink": + qtl_results = self.run_plink() elif self.mapping_method == "pylmm": #self.qtl_results = self.gen_data(tempdata) qtl_results = self.gen_data(str(temp_uuid)) @@ -151,6 +153,10 @@ class MarkerRegression(object): # # + def run_plink(self): + + os.chdir("/home/zas1024/plink") + #def gen_data(self, tempdata): def gen_data(self, temp_uuid): """Generates p-values for each marker""" diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index db8d4f1a..6f0ff44b 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -98,7 +98,10 @@ class ShowTrait(object): hddn['trait_id'] = self.trait_id hddn['dataset'] = self.dataset.name hddn['method'] = "pylmm" - + hddn['mapping_display_all'] = True + hddn['suggestive'] = 0 + hddn['maf'] = 0.01 + # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self self.hddn = hddn diff --git a/wqflask/wqflask/static/new/css/bar_chart.css b/wqflask/wqflask/static/new/css/bar_chart.css index c8e081f9..3e6e7bd6 100755 --- a/wqflask/wqflask/static/new/css/bar_chart.css +++ b/wqflask/wqflask/static/new/css/bar_chart.css @@ -9,7 +9,7 @@ fill: steelblue; shape-rendering: crispEdges; } - +/* .x.axis path { display: none; -} \ No newline at end of file +}*/ \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee index 6c1e65e9..98f89ac6 100755 --- a/wqflask/wqflask/static/new/javascript/histogram.coffee +++ b/wqflask/wqflask/static/new/javascript/histogram.coffee @@ -41,13 +41,15 @@ class Histogram create_x_scale: () -> console.log("min/max:", d3.min(@sample_vals) + "," + d3.max(@sample_vals)) - if (d3.min(@sample_vals) < 0) - min_domain = d3.min(@sample_vals) - else - min_domain = 0 + x0 = Math.max(-d3.min(@sample_vals), d3.max(@sample_vals)) + #if (d3.min(@sample_vals) < 0) + # min_domain = d3.min(@sample_vals) + #else + # min_domain = 0 @x_scale = d3.scale.linear() - .domain([min_domain, parseFloat(d3.max(@sample_vals))]) - .range([0, @plot_width]) + .domain([d3.min(@sample_vals), d3.max(@sample_vals)]) + .range([0, @plot_width]) + .nice() get_histogram_data: () -> console.log("sample_vals:", @sample_vals) @@ -62,6 +64,7 @@ class Histogram create_graph: () -> @add_x_axis() + @add_y_axis() @add_bars() add_x_axis: () -> @@ -74,11 +77,32 @@ class Histogram .attr("transform", "translate(0," + @plot_height + ")") .call(x_axis) + #add_y_axis: () -> + # y_axis = d3.svg.axis() + # .scale(@y_scale) + # .orient("left") + # .ticks(5) + # + # @svg.append("g") + # .attr("class", "y axis") + # #.attr("transform", "translate(0," + @plot_width + ")") + # .call(y_axis) + + add_y_axis: () -> - y_axis = d3.svg.axis() + yAxis = d3.svg.axis() .scale(@y_scale) .orient("left") .ticks(5) + + @svg.append("g") + .attr("class", "y axis") + .call(yAxis) + .append("text") + .attr("transform", "rotate(-90)") + .attr("y", 6) + .attr("dy", ".71em") + .style("text-anchor", "end") add_bars: () -> console.log("bar_width:", @x_scale(@histogram_data[0].dx)) diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js index 1603cb77..d8067ced 100755 --- a/wqflask/wqflask/static/new/javascript/histogram.js +++ b/wqflask/wqflask/static/new/javascript/histogram.js @@ -55,14 +55,10 @@ }; Histogram.prototype.create_x_scale = function() { - var min_domain; + var x0; console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals)); - if (d3.min(this.sample_vals) < 0) { - min_domain = d3.min(this.sample_vals); - } else { - min_domain = 0; - } - return this.x_scale = d3.scale.linear().domain([min_domain, parseFloat(d3.max(this.sample_vals))]).range([0, this.plot_width]); + x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals)); + return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice(); }; Histogram.prototype.get_histogram_data = function() { @@ -82,6 +78,7 @@ Histogram.prototype.create_graph = function() { this.add_x_axis(); + this.add_y_axis(); return this.add_bars(); }; @@ -92,8 +89,9 @@ }; Histogram.prototype.add_y_axis = function() { - var y_axis; - return y_axis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + var yAxis; + yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end"); }; Histogram.prototype.add_bars = function() { diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 84e465e8..a410baf3 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -204,6 +204,7 @@ $ -> name = $.trim(name) real_value = $(row).find('.edit_sample_value').val() console.log("real_value:", real_value) + checkbox = $(row).find(".edit_sample_checkbox") checked = $(checkbox).attr('checked') diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee index f1024cd1..1d375686 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee @@ -56,6 +56,9 @@ $ -> console.log("In interval mapping") $("#progress_bar_container").modal() url = "/interval_mapping" + $('input[name=method]').val("reaper") + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')) + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')) form_data = $('#trait_data_form').serialize() console.log("form_data is:", form_data) $.ajax( @@ -116,9 +119,41 @@ $ -> return false ) + $("#plink_compute").click(() => + url = "/marker_regression" + $('input[name=method]').val("plink") + $('input[name=mapping_display_all]').val($('input[name=display_all_plink]')) + $('input[name=suggestive]').val($('input[name=suggestive_plink]')) + $('input[name=maf]').val($('input[name=maf_plink]')) + form_data = $('#trait_data_form').serialize() + console.log("form_data is:", form_data) + $.ajax( + type: "POST" + url: url + data: form_data + error: (xhr, ajaxOptions, thrownError) => + alert("Sorry, an error occurred") + console.log(xhr) + clearInterval(this.my_timer) + $('#progress_bar_container').modal('hide') + $("body").html("We got an error.") + success: (data) => + clearInterval(this.my_timer) + $('#progress_bar_container').modal('hide') + $("body").html(data) + ) + console.log("settingInterval") + + this.my_timer = setInterval(get_progress, 1000) + return false + ) + $("#gemma_compute").click(() => url = "/marker_regression" $('input[name=method]').val("gemma") + $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]')) + $('input[name=suggestive]').val($('input[name=suggestive_gemma]')) + $('input[name=maf]').val($('input[name=maf_gemma]')) form_data = $('#trait_data_form').serialize() console.log("form_data is:", form_data) $.ajax( diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index a5a49ace..dbc26e3b 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -67,6 +67,9 @@ console.log("In interval mapping"); $("#progress_bar_container").modal(); url = "/interval_mapping"; + $('input[name=method]').val("reaper"); + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); form_data = $('#trait_data_form').serialize(); console.log("form_data is:", form_data); $.ajax({ @@ -127,10 +130,43 @@ _this.my_timer = setInterval(get_progress, 1000); return false; }); + $("#plink_compute").click(function() { + var form_data, url; + url = "/marker_regression"; + $('input[name=method]').val("plink"); + $('input[name=mapping_display_all]').val($('input[name=display_all_plink]')); + $('input[name=suggestive]').val($('input[name=suggestive_plink]')); + $('input[name=maf]').val($('input[name=maf_plink]')); + form_data = $('#trait_data_form').serialize(); + console.log("form_data is:", form_data); + $.ajax({ + type: "POST", + url: url, + data: form_data, + error: function(xhr, ajaxOptions, thrownError) { + alert("Sorry, an error occurred"); + console.log(xhr); + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + return $("body").html("We got an error."); + }, + success: function(data) { + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + return $("body").html(data); + } + }); + console.log("settingInterval"); + _this.my_timer = setInterval(get_progress, 1000); + return false; + }); $("#gemma_compute").click(function() { var form_data, url; url = "/marker_regression"; $('input[name=method]').val("gemma"); + $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]')); + $('input[name=suggestive]').val($('input[name=suggestive_gemma]')); + $('input[name=maf]').val($('input[name=maf_gemma]')); form_data = $('#trait_data_form').serialize(); console.log("form_data is:", form_data); $.ajax({ diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index e15d043b..ff05e859 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -69,38 +69,98 @@ + - {% endblock %} diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index cc995f2f..f380988e 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -9,6 +9,9 @@
  • Marker Regression
    • +
  • + PLINK +
  • GEMMA
    • @@ -114,20 +117,20 @@
    -
    - +
    @@ -151,32 +154,74 @@ + +
    -
    - +
    -
    - +
    -- cgit v1.2.3