From 9c272d1b2342b8f8e62927e9f1bfab9594946ab4 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Mon, 17 Nov 2014 17:22:33 +0000 Subject: Just more changes converting to bootstrap 3 --- web/gemma/HLC.fam | 740 +- web/gemma/output/HLC_output.assoc.txt | 546698 +++++++++--------- web/gemma/output/HLC_output.log.txt | 22 +- wqflask/base/data_set.py | 2 +- .../wqflask/marker_regression/marker_regression.py | 2 +- .../static/new/javascript/create_lodchart.coffee | 174 +- .../wqflask/static/new/javascript/panelutil.coffee | 712 +- .../new/javascript/show_trait_mapping_tools.coffee | 2 +- .../new/javascript/show_trait_mapping_tools.js | 4 +- wqflask/wqflask/templates/base.html | 2 +- wqflask/wqflask/templates/collections/view.html | 35 +- wqflask/wqflask/templates/index_page.html | 20 +- .../wqflask/templates/new_security/login_user.html | 34 +- wqflask/wqflask/templates/show_trait.html | 21 +- wqflask/wqflask/templates/show_trait_details.html | 4 +- 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1.599585e+01 8.657120e-01 +23 rs1154823 148191955 8 T C 0.095 4.967576e+01 1.232664e+02 1.606876e+01 6.871544e-01 +23 rs5936294 148271976 16 C T 0.307 1.156813e+02 7.729594e+01 1.566488e+01 1.352389e-01 +23 rs544682 148300970 10 C A 0.157 -3.475868e+01 1.012821e+02 1.591514e+01 7.316276e-01 +23 rs5980360 148391694 18 G A 0.077 -1.739608e+01 1.345008e+02 1.590862e+01 8.971513e-01 +23 rs16995456 148397958 12 C A 0.078 4.549636e-01 1.319248e+02 1.594380e+01 9.972500e-01 +23 rs12013571 148417806 12 G A 0.151 -7.546252e+00 1.040250e+02 1.594384e+01 9.422042e-01 +23 rs2233048 148474910 5 T C 0.474 -5.527189e+01 7.306445e+01 1.560875e+01 4.497798e-01 +23 rs16992983 148592207 16 G C 0.049 6.284287e+01 1.754336e+02 1.600773e+01 7.203606e-01 +23 rs11798728 148636925 10 T A 0.073 6.406819e+01 1.386250e+02 1.591342e+01 6.441967e-01 +23 rs9780782 149077884 21 G A 0.092 1.268915e+02 1.301348e+02 1.576445e+01 3.300764e-01 +23 rs7054236 149181640 8 T C 0.039 3.283834e+01 1.913773e+02 1.596797e+01 8.638419e-01 +23 rs5970576 149220526 12 C T 0.223 -2.103599e+02 8.664010e+01 1.549490e+01 1.559766e-02 +23 rs502696 149289341 21 T C 0.317 8.407008e+01 8.040592e+01 1.612988e+01 2.963536e-01 +23 rs2266828 149294660 0 T C 0.367 9.679545e+01 7.355070e+01 1.576793e+01 1.888710e-01 +23 rs17318805 149295318 18 T C 0.144 9.015187e+01 1.066881e+02 1.611280e+01 3.985840e-01 +23 rs2266831 149295343 11 G A 0.363 9.618172e+01 7.537031e+01 1.584576e+01 2.026093e-01 +23 rs2283740 149307364 15 T C 0.183 1.204102e+01 9.331073e+01 1.598591e+01 8.973853e-01 +23 rs2073043 149312586 4 G A 0.163 5.911592e+01 9.647825e+01 1.615166e+01 5.403771e-01 +23 rs500294 149335565 8 T C 0.279 -1.449285e+01 7.985022e+01 1.591099e+01 8.560613e-01 +23 rs222347 149439064 4 T C 0.065 -1.444564e+02 1.461180e+02 1.594464e+01 3.234075e-01 +23 rs6526186 149461755 11 C T 0.493 -1.555378e+01 7.455786e+01 1.589706e+01 8.348499e-01 +23 rs16996690 149476064 0 T C 0.107 -7.392699e+01 1.166380e+02 1.599128e+01 5.265422e-01 +23 rs10521889 149507429 1 G T 0.081 2.651162e+01 1.286583e+02 1.595125e+01 8.368410e-01 +23 rs5925403 149514767 16 T C 0.296 1.458600e+01 8.088371e+01 1.592448e+01 8.569772e-01 +23 rs5925408 149547779 4 G A 0.320 -2.300153e+01 7.706789e+01 1.601718e+01 7.654995e-01 +23 rs5924843 149630957 1 G A 0.059 1.359097e+02 1.539094e+02 1.614579e+01 3.777086e-01 +23 rs4240082 149688117 7 C T 0.426 1.251107e+02 7.169043e+01 1.578655e+01 8.168125e-02 +23 rs4489434 149692058 8 T G 0.118 3.101203e+02 1.135483e+02 1.570091e+01 6.573586e-03 +23 rs10521890 149765715 9 A G 0.165 -2.479610e+01 9.970152e+01 1.589653e+01 8.037104e-01 +23 rs237378 149770769 7 G A 0.080 8.412827e+01 1.391903e+02 1.615363e+01 5.458922e-01 +23 rs12845940 149858262 20 A T 0.413 -7.152277e+01 7.521541e+01 1.570497e+01 3.421926e-01 +23 rs5925480 149869160 5 C T 0.276 -5.725389e+01 8.145617e+01 1.577960e+01 4.825155e-01 +23 rs726397 149870998 21 T C 0.401 -6.432217e+01 7.570699e+01 1.584613e+01 3.960147e-01 +23 rs3866985 149890196 16 T C 0.103 -1.247495e+02 1.217766e+02 1.566343e+01 3.062231e-01 +23 rs3912366 149890696 10 C T 0.302 1.371152e+02 8.000020e+01 1.501284e+01 8.726963e-02 +23 rs5925493 149896918 19 C T 0.293 -1.790617e+01 8.094856e+01 1.591620e+01 8.250396e-01 +23 rs4644439 149903546 3 A T 0.283 -1.399303e+01 7.965685e+01 1.592753e+01 8.606397e-01 +23 rs3853550 149915046 4 C T 0.285 -1.320543e+01 7.977229e+01 1.592679e+01 8.685984e-01 +23 rs180486 149991156 5 A C 0.083 -6.842402e+01 1.322455e+02 1.605678e+01 6.051451e-01 +23 rs180487 149991301 4 T A 0.085 -6.709284e+01 1.316128e+02 1.609606e+01 6.104742e-01 +23 rs7878475 150001740 9 C T 0.078 2.213764e+02 1.342695e+02 1.619871e+01 9.993855e-02 +23 rs1930693 150024093 9 A C 0.322 -3.166999e+01 7.737095e+01 1.622410e+01 6.825062e-01 +23 rs1149370 150077385 5 C T 0.213 -6.588842e+01 8.854742e+01 1.596406e+01 4.572253e-01 +23 rs926046 150086290 8 G A 0.358 -4.172503e+01 7.575967e+01 1.590481e+01 5.820909e-01 +23 rs12557937 150086546 5 A G 0.052 -3.405087e+01 1.623720e+02 1.595912e+01 8.339953e-01 +23 rs1202917 150110209 5 C A 0.476 -8.188574e+00 7.201732e+01 1.594601e+01 9.095271e-01 +23 rs17319461 150156863 4 T C 0.311 7.689964e+01 7.839339e+01 1.574905e+01 3.271777e-01 +23 rs5970014 150165208 12 A G 0.431 1.291741e+02 7.338977e+01 1.519282e+01 7.910829e-02 +23 rs16995944 150182119 14 A C 0.217 -4.622116e+01 8.600540e+01 1.612175e+01 5.912577e-01 +23 rs17253640 150182399 2 G A 0.079 3.289539e+01 1.309228e+02 1.523579e+01 8.017361e-01 +23 rs4828564 150196949 12 A G 0.455 -7.776721e+01 7.241841e+01 1.565951e+01 2.834949e-01 +23 rs4828565 150197007 4 C A 0.473 9.886079e+01 7.203754e+01 1.586668e+01 1.706780e-01 +23 rs5924937 150258484 13 C G 0.454 -5.322724e+01 7.312830e+01 1.574952e+01 4.670995e-01 +23 rs5969796 150325411 2 C T 0.435 1.511583e+02 7.217635e+01 1.541773e+01 3.682574e-02 +23 rs5970056 150328777 8 G C 0.041 -2.207562e+01 1.780505e+02 1.595325e+01 9.013856e-01 +23 rs5924646 150412863 11 A G 0.446 1.471159e+02 7.276407e+01 1.528490e+01 4.382104e-02 +23 rs7885463 150444039 5 A G 0.352 1.266050e+02 7.583576e+01 1.535819e+01 9.576194e-02 +23 rs7887266 150444214 11 G A 0.405 1.108811e+02 7.476847e+01 1.550646e+01 1.388176e-01 +23 rs5924659 150488108 17 T C 0.380 -1.982412e+01 7.571869e+01 1.600155e+01 7.935927e-01 +23 rs5924997 150518260 16 T C 0.236 -3.169441e+01 8.531596e+01 1.697992e+01 7.104544e-01 +23 rs1554914 150549224 9 G T 0.233 5.080211e+01 8.682615e+01 1.597396e+01 5.587900e-01 +23 rs6627452 150564760 14 A G 0.350 -5.151438e+00 7.581499e+01 1.595387e+01 9.458594e-01 +23 rs12839777 150571582 13 A G 0.292 -8.891597e+01 7.996004e+01 1.598603e+01 2.667646e-01 +23 rs5970100 150576381 17 A C 0.080 -3.735000e+00 1.376104e+02 1.597026e+01 9.783593e-01 +23 rs5969818 150583736 10 C G 0.079 -6.366510e+00 1.384610e+02 1.596814e+01 9.633474e-01 +23 rs5925036 150608736 14 A G 0.213 5.616129e+01 8.720291e+01 1.548651e+01 5.199034e-01 +23 3883889 150688242 12 T A 0.087 -2.094975e+00 1.387249e+02 1.595948e+01 9.879582e-01 +23 3883890 150688297 7 T A 0.090 -8.157674e+01 1.292287e+02 1.608191e+01 5.282107e-01 +23 rs12843815 150692967 13 T C 0.403 -1.110415e+02 7.474296e+01 1.590833e+01 1.381145e-01 +23 rs6627483 150709289 7 T C 0.118 -7.923747e+01 1.161552e+02 1.602862e+01 4.955038e-01 +23 rs933191 150767597 2 G A 0.111 -5.876792e+01 1.154323e+02 1.599801e+01 6.109381e-01 +23 rs7882041 150779636 8 G T 0.150 -2.116297e+01 1.011511e+02 1.594566e+01 8.343757e-01 +23 rs5970169 150782245 17 T G 0.128 1.423191e+01 1.118851e+02 1.596447e+01 8.988414e-01 +23 rs12011671 150795532 7 C T 0.327 -8.436438e+01 7.775560e+01 1.585939e+01 2.785392e-01 +23 rs2157012 150833514 6 G C 0.223 1.127750e+01 8.729036e+01 1.594616e+01 8.972643e-01 +23 rs11094534 150853849 4 T C 0.215 1.389012e+01 8.815796e+01 1.594238e+01 8.748788e-01 +23 rs5970194 150911182 10 A G 0.210 4.349438e+01 8.987088e+01 1.591011e+01 6.286598e-01 +23 rs1844894 150932710 11 G A 0.130 1.164288e+02 1.095043e+02 1.575059e+01 2.882792e-01 +23 rs210584 150975511 21 G A 0.339 6.201055e+01 7.574115e+01 1.557884e+01 4.134069e-01 +23 rs1491793 151004671 14 A T 0.249 2.808256e+01 8.339426e+01 1.585065e+01 7.364757e-01 +23 rs994424 151052347 8 C T 0.161 -1.399508e+02 9.899217e+01 1.627391e+01 1.581654e-01 +23 rs7064104 151062197 5 G A 0.168 -1.225577e+02 9.652862e+01 1.619805e+01 2.049036e-01 +23 3884087 151116918 12 C T 0.090 -9.956951e+01 1.208977e+02 1.602969e+01 4.106375e-01 +23 rs5925155 151128485 7 G A 0.339 -5.197098e+01 7.488510e+01 1.639560e+01 4.880553e-01 +23 rs4828696 151252563 16 T C 0.384 1.408646e+02 7.486897e+01 1.574425e+01 6.058961e-02 +23 rs6627595 151288570 10 C G 0.415 2.321937e+01 7.400967e+01 1.597392e+01 7.538768e-01 +23 rs6627611 151439733 8 G A 0.329 1.772231e+01 7.760088e+01 1.595223e+01 8.194625e-01 +23 rs5924753 151488575 8 C T 0.470 -1.254451e+02 7.301818e+01 1.615862e+01 8.652526e-02 +23 rs2471773 151569922 5 T C 0.444 7.007829e+01 7.342114e+01 1.601491e+01 3.403883e-01 +23 rs2515832 151572621 2 C G 0.446 6.847071e+01 7.302342e+01 1.597426e+01 3.489547e-01 +23 rs6526129 151652671 1 A G 0.089 -5.067570e+01 1.244177e+02 1.588447e+01 6.839906e-01 +23 rs3088344 151666353 7 T G 0.120 -1.548395e+01 1.156839e+02 1.593040e+01 8.935869e-01 +23 rs6627690 151672683 4 A T 0.040 -2.864594e+01 1.831174e+02 1.595959e+01 8.757646e-01 +23 rs12845949 151688319 21 A G 0.284 1.000552e+01 8.033887e+01 1.594362e+01 9.009455e-01 +23 rs5970391 151712954 6 T G 0.493 2.017695e+01 7.213036e+01 1.592415e+01 7.798215e-01 +23 rs6526138 151718162 20 A G 0.299 4.869532e+00 8.096137e+01 1.595322e+01 9.520673e-01 +23 rs5925239 151729952 2 C T 0.213 -3.659785e+01 8.565786e+01 1.592854e+01 6.694091e-01 +23 rs5969921 151731439 20 C T 0.134 -1.665903e+00 1.139017e+02 1.595588e+01 9.883376e-01 +23 rs2071257 151759270 3 G T 0.204 -2.694526e+01 8.845194e+01 1.596459e+01 7.607958e-01 +23 rs10126824 151778651 8 T C 0.085 -1.585695e+02 1.319031e+02 1.577807e+01 2.299684e-01 +23 rs5925268 151808635 21 T C 0.267 -4.304857e+01 8.178030e+01 1.581850e+01 5.988899e-01 +23 rs12560037 151839176 19 T C 0.331 -9.374265e+01 7.608673e+01 1.598719e+01 2.186117e-01 +23 rs2382883 151873256 3 A G 0.065 4.962433e+01 1.434923e+02 1.593669e+01 7.296396e-01 +23 rs6627738 151900925 14 C T 0.059 1.454160e+02 1.509728e+02 1.586812e+01 3.359982e-01 +23 rs4828744 151925407 4 G A 0.070 8.377843e+01 1.389327e+02 1.593464e+01 5.468208e-01 +23 rs4828747 151929154 8 C T 0.074 1.066877e+02 1.371978e+02 1.594889e+01 4.372258e-01 +23 rs2008144 151966996 4 A G 0.069 7.890449e+01 1.409684e+02 1.592538e+01 5.759572e-01 +23 rs5925336 151987489 20 T C 0.189 4.454084e+01 9.338956e+01 1.596915e+01 6.336528e-01 +23 rs1894342 151987996 11 G A 0.066 1.193728e+02 1.450988e+02 1.591428e+01 4.111400e-01 +23 rs1557505 151992064 2 G A 0.181 4.253441e+01 9.270232e+01 1.597832e+01 6.465923e-01 +23 rs5924813 151995603 7 C T 0.060 1.789484e+02 1.516085e+02 1.575204e+01 2.385282e-01 +23 rs2012435 152010745 2 T C 0.068 1.011081e+02 1.414283e+02 1.590293e+01 4.750588e-01 +23 rs2012436 152010777 2 G C 0.068 1.011081e+02 1.414283e+02 1.590293e+01 4.750588e-01 +23 rs5925368 152033116 13 G A 0.056 5.376141e+01 1.609354e+02 1.591488e+01 7.385023e-01 +23 rs6627772 152053967 5 A G 0.327 -1.864113e+02 7.490601e+01 1.562485e+01 1.320654e-02 +23 rs995423 152085362 13 A T 0.488 -6.090244e+01 7.253517e+01 1.593372e+01 4.015900e-01 +23 rs1894354 152089815 0 T C 0.177 -4.725626e+01 9.573306e+01 1.615418e+01 6.218258e-01 +23 rs5986911 152351829 6 T A 0.036 -2.349732e+02 2.052692e+02 1.608473e+01 2.529747e-01 +23 rs5945145 152351894 5 C T 0.405 -2.296156e+01 7.337206e+01 1.600948e+01 7.544745e-01 +23 rs4898424 152360329 16 G T 0.274 4.684036e+00 8.221131e+01 1.594832e+01 9.545914e-01 +23 rs4898428 152397543 12 A G 0.134 -5.955819e+01 1.092205e+02 1.596693e+01 5.858318e-01 +23 rs3761536 152427138 16 A T 0.178 -2.681676e+00 9.622300e+01 1.595431e+01 9.777794e-01 +23 rs5987140 152521101 20 C T 0.111 5.193335e+01 1.213441e+02 1.595543e+01 6.688794e-01 +23 rs2266887 152760433 8 T G 0.203 7.718603e+01 9.181158e+01 1.588840e+01 4.009886e-01 +23 rs7884370 152843727 5 G A 0.041 2.460087e+02 1.782285e+02 1.583888e+01 1.682200e-01 +23 rs1734791 152851766 13 T A 0.158 -1.149214e+01 1.001773e+02 1.603198e+01 9.087229e-01 +23 rs766420 153075250 6 C G 0.220 6.280638e+01 8.755395e+01 1.608354e+01 4.735554e-01 +23 rs766419 153075507 6 C T 0.219 4.411589e+01 8.756093e+01 1.602046e+01 6.146413e-01 +23 rs2239467 153076140 14 G A 0.224 5.717691e+01 8.783936e+01 1.606658e+01 5.154461e-01 +23 rs4898494 153174968 5 T A 0.108 2.427077e+02 1.155737e+02 1.590925e+01 3.631549e-02 +23 rs4898348 153450097 18 T C 0.231 2.775226e+02 8.732649e+01 1.621495e+01 1.591316e-03 +23 rs5945109 153471452 8 G A 0.377 1.691606e+02 7.536096e+01 1.619144e+01 2.530292e-02 +23 rs5945122 153737610 8 C A 0.135 1.924957e+01 1.071433e+02 1.598439e+01 8.575037e-01 +23 rs2051161 153849554 3 G C 0.383 1.635377e+02 7.466881e+01 1.599425e+01 2.905430e-02 +23 3885427 154017791 18 G A 0.232 -4.297558e+01 8.482810e+01 1.569159e+01 6.126845e-01 +23 rs475025 154048640 3 G A 0.243 -2.214191e+01 8.269887e+01 1.592490e+01 7.890283e-01 +23 rs6420603 154316683 14 G A 0.029 -8.620842e+01 2.205232e+02 1.595658e+01 6.960472e-01 +23 rs574386 154411192 9 C T 0.240 -4.051368e+01 8.233156e+01 1.565906e+01 6.229171e-01 diff --git a/web/gemma/output/HLC_output.log.txt b/web/gemma/output/HLC_output.log.txt index 773e86c4..fc7975f4 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 = -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 +## REMLE log-likelihood in the null model = -3650.56 +## MLE log-likelihood in the null model = -3657.67 +## pve estimate in the null model = 0.840196 +## se(pve) in the null model = 0.106606 +## vg estimate in the null model = 4.2245e+06 +## ve estimate in the null model = 265756 +## beta estimate in the null model = 1202.14 +## se(beta) = 24.9475 ## ## Computation Time: -## total computation time = 2.61417 min +## total computation time = 2.73533 min ## computation time break down: ## time on eigen-decomposition = 0.00166667 min -## time on calculating UtX = 0.412 min -## time on optimization = 2.03567 min +## time on calculating UtX = 0.417333 min +## time on optimization = 2.146 min ## diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 685cd648..7e187802 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -79,7 +79,7 @@ class Dataset_Types(object): def __init__(self): self.datasets = {} - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" + file_name = "/home/zas1024/gene/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 7f215d9b..60221c05 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -513,7 +513,7 @@ class MarkerRegression(object): p_value = float(line_list[-1]) if threshold_p_value >= 0 and threshold_p_value <= 1: if p_value < threshold_p_value: - p_value_dict[snp] = p_value + p_value_dict[snp] = float(p_value) if plink_results.has_key(chr_name): value_list = plink_results[chr_name] diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee index 2d5e3acb..76be5490 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee @@ -1,87 +1,87 @@ -create_manhattan_plot = -> - h = 500 - w = 1200 - margin = {left:60, top:40, right:40, bottom: 40, inner:5} - halfh = (h+margin.top+margin.bottom) - totalh = halfh*2 - totalw = (w+margin.left+margin.right) - if 'additive' of js_data - additive = js_data.additive - else - additive = false - - console.log("js_data:", js_data) - - # simplest use - #d3.json "data.json", (data) -> - mychart = lodchart().lodvarname("lod.hk") - .height(h) - .width(w) - .margin(margin) - .ylab("LOD score") - .manhattanPlot(js_data.manhattan_plot) - #.additive(additive) - - data = js_data.json_data - - d3.select("div#topchart") - .datum(data) - .call(mychart) - - # grab chromosome rectangles; color pink on hover - chrrect = mychart.chrSelect() - chrrect.on "mouseover", -> - d3.select(this).attr("fill", "#E9CFEC") - .on "mouseout", (d,i) -> - d3.select(this).attr("fill", -> - return "#F1F1F9" if i % 2 - "#FBFBFF") - - # animate points at markers on click - mychart.markerSelect() - .on "click", (d) -> - r = d3.select(this).attr("r") - d3.select(this) - .transition().duration(500).attr("r", r*3) - .transition().duration(500).attr("r", r) - -create_manhattan_plot() - -$("#export").click => - #Get d3 SVG element - svg = $("#topchart").find("svg")[0] - - #Extract SVG text string - svg_xml = (new XMLSerializer).serializeToString(svg) - console.log("svg_xml:", svg_xml) - - #Set filename - filename = "manhattan_plot_" + js_data.this_trait - - #Make a form with the SVG data - form = $("#exportform") - form.find("#data").val(svg_xml) - form.find("#filename").val(filename) - form.submit() - -$("#export_pdf").click => - - #$('#topchart').remove() - #$('#chart_container').append('
') - #create_interval_map() - - #Get d3 SVG element - svg = $("#topchart").find("svg")[0] - - #Extract SVG text string - svg_xml = (new XMLSerializer).serializeToString(svg) - console.log("svg_xml:", svg_xml) - - #Set filename - filename = "manhattan_plot_" + js_data.this_trait - - #Make a form with the SVG data - form = $("#exportpdfform") - form.find("#data").val(svg_xml) - form.find("#filename").val(filename) - form.submit() +create_manhattan_plot = -> + h = 500 + w = 1200 + margin = {left:60, top:40, right:40, bottom: 40, inner:5} + halfh = (h+margin.top+margin.bottom) + totalh = halfh*2 + totalw = (w+margin.left+margin.right) + if 'additive' of js_data + additive = js_data.additive + else + additive = false + + console.log("js_data:", js_data) + + # simplest use + #d3.json "data.json", (data) -> + mychart = lodchart().lodvarname("lod.hk") + .height(h) + .width(w) + .margin(margin) + .ylab("LOD score") + .manhattanPlot(js_data.manhattan_plot) + #.additive(additive) + + data = js_data.json_data + + d3.select("div#topchart") + .datum(data) + .call(mychart) + + # grab chromosome rectangles; color pink on hover + chrrect = mychart.chrSelect() + chrrect.on "mouseover", -> + d3.select(this).attr("fill", "#E9CFEC") + .on "mouseout", (d,i) -> + d3.select(this).attr("fill", -> + return "#F1F1F9" if i % 2 + "#FBFBFF") + + # animate points at markers on click + mychart.markerSelect() + .on "click", (d) -> + r = d3.select(this).attr("r") + d3.select(this) + .transition().duration(500).attr("r", r*3) + .transition().duration(500).attr("r", r) + +create_manhattan_plot() + +$("#export").click => + #Get d3 SVG element + svg = $("#topchart").find("svg")[0] + + #Extract SVG text string + svg_xml = (new XMLSerializer).serializeToString(svg) + console.log("svg_xml:", svg_xml) + + #Set filename + filename = "manhattan_plot_" + js_data.this_trait + + #Make a form with the SVG data + form = $("#exportform") + form.find("#data").val(svg_xml) + form.find("#filename").val(filename) + form.submit() + +$("#export_pdf").click => + + #$('#topchart').remove() + #$('#chart_container').append('
') + #create_interval_map() + + #Get d3 SVG element + svg = $("#topchart").find("svg")[0] + + #Extract SVG text string + svg_xml = (new XMLSerializer).serializeToString(svg) + console.log("svg_xml:", svg_xml) + + #Set filename + filename = "manhattan_plot_" + js_data.this_trait + + #Make a form with the SVG data + form = $("#exportpdfform") + form.find("#data").val(svg_xml) + form.find("#filename").val(filename) + form.submit() diff --git a/wqflask/wqflask/static/new/javascript/panelutil.coffee b/wqflask/wqflask/static/new/javascript/panelutil.coffee index d1eb83e5..a3bc0b44 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.coffee +++ b/wqflask/wqflask/static/new/javascript/panelutil.coffee @@ -1,357 +1,357 @@ -# A variety of utility functions used by the different panel functions - -# determine rounding of axis labels -formatAxis = (d, extra_digits=0) -> - d = d[1] - d[0] - ndig = Math.floor( Math.log(d % 10) / Math.log(10) ) - ndig = 0 if ndig > 0 - ndig = Math.abs(ndig) + extra_digits - d3.format(".#{ndig}f") - -# unique values of array (ignore nulls) -unique = (x) -> - output = {} - output[v] = v for v in x when v - output[v] for v of output - -# Pull out a variable (column) from a two-dimensional array -pullVarAsArray = (data, variable) -> - v = [] - for i of data - v = v.concat data[i][variable] - v - - -# reorganize lod/pos by chromosome -# lodvarname==null -> case for multiple LOD columns (lodheatmap) -# lodvarname provided -> case for one LOD column (lodchart) -reorgLodData = (data, lodvarname=null) -> - data.posByChr = {} - data.lodByChr = {} - - for chr,i in data.chrnames - #console.log("chr:", chr) - data.posByChr[chr[0]] = [] - data.lodByChr[chr[0]] = [] - for pos, j in data.pos - if data.chr[j].toString() == chr[0] - #console.log(data.chr[j] + " AND " + chr[0]) - data.posByChr[chr[0]].push(pos) - data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames) - lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) - data.lodByChr[chr[0]].push(lodval) - - #console.log("data.posByChr:", data.posByChr) - - if lodvarname? - data.markers = [] - for marker,i in data.markernames - if marker != "" - data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]}) - - data - -# calculate chromosome start/end + scales, for heat map -chrscales = (data, width, chrGap, leftMargin, pad4heatmap) -> - # start and end of chromosome positions - chrStart = [] - chrEnd = [] - chrLength = [] - totalChrLength = 0 - maxd = 0 - for chr in data.chrnames - d = maxdiff(data.posByChr[chr[0]]) - maxd = d if d > maxd - - rng = d3.extent(data.posByChr[chr[0]]) - chrStart.push(rng[0]) - chrEnd.push(rng[1]) - L = rng[1] - rng[0] - chrLength.push(L) - totalChrLength += L - - # adjust lengths for heatmap - if pad4heatmap - data.recwidth = maxd - chrStart = chrStart.map (x) -> x-maxd/2 - chrEnd = chrEnd.map (x) -> x+maxd/2 - chrLength = chrLength.map (x) -> x+maxd - totalChrLength += (chrLength.length*maxd) - - # break up x axis into chromosomes by length, with gaps - data.chrStart = [] - data.chrEnd = [] - cur = leftMargin - cur += chrGap/2 unless pad4heatmap - data.xscale = {} - for chr,i in data.chrnames - data.chrStart.push(cur) - w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i]) - data.chrEnd.push(cur + w) - cur = data.chrEnd[i] + chrGap - # x-axis scales, by chromosome - data.xscale[chr[0]] = d3.scale.linear() - .domain([chrStart[i], chrEnd[i]]) - .range([data.chrStart[i], data.chrEnd[i]]) - - # return data with new stuff added - data - - -# reorganize lod/pos by chromosome -# lodvarname==null -> case for multiple LOD columns (lodheatmap) -# lodvarname provided -> case for one LOD column (lodchart) -#reorgLodData = (data, lodvarname=null) -> -# data.posByChr = {} -# data.lodByChr = {} -# -# #console.log("data.chr", data.chr) -# #console.log("data.chrnames:", data.chrnames) -# the_chr = "0" -# for chr,i in data.chrnames -# data.posByChr[chr] = [] -# data.lodByChr[chr] = [] -# for pos,j in data.pos -# console.log("data.chr[j][0]:", data.chr[j][0]) -# if data.chr[j][0] == chr -# console.log("IS EQUAL") -# data.posByChr[chr].push(pos) -# data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames) -# lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) -# data.lodByChr[chr].push(lodval) -# -# if lodvarname? -# data.markers = [] -# for marker,i in data.markernames -# if marker != "" -# data.markers.push({name:marker, chr:data.chr[i][0], pos:data.pos[i], lod:data[lodvarname][i]}) -# -# data - -# calculate chromosome start/end + scales, for heat map -#chrscales = (data, width, chrGap, leftMargin, pad4heatmap) -> -# # start and end of chromosome positions -# chrStart = [] -# chrEnd = [] -# chrLength = [] -# totalChrLength = 0 -# maxd = 0 -# for chr in data.chrnames -# d = maxdiff(data.posByChr[chr]) -# maxd = d if d > maxd -# -# rng = d3.extent(data.posByChr[chr]) -# chrStart.push(rng[0]) -# chrEnd.push(rng[1]) -# L = rng[1] - rng[0] -# chrLength.push(L) -# totalChrLength += L -# -# # adjust lengths for heatmap -# if pad4heatmap -# data.recwidth = maxd -# chrStart = chrStart.map (x) -> x-maxd/2 -# chrEnd = chrEnd.map (x) -> x+maxd/2 -# chrLength = chrLength.map (x) -> x+maxd -# totalChrLength += (chrLength.length*maxd) -# -# # break up x axis into chromosomes by length, with gaps -# data.chrStart = [] -# data.chrEnd = [] -# cur = leftMargin -# cur += chrGap/2 unless pad4heatmap -# data.xscale = {} -# for chr,i in data.chrnames -# data.chrStart.push(cur) -# w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i]) -# data.chrEnd.push(cur + w) -# cur = data.chrEnd[i] + chrGap -# # x-axis scales, by chromosome -# data.xscale[chr] = d3.scale.linear() -# .domain([chrStart[i], chrEnd[i]]) -# .range([data.chrStart[i], data.chrEnd[i]]) -# -# # return data with new stuff added -# data - -# Select a set of categorical colors -# ngroup is positive integer -# palette = "dark" or "pastel" -selectGroupColors = (ngroup, palette) -> - return [] if ngroup == 0 - - if palette == "dark" - return ["slateblue"] if ngroup == 1 - return ["MediumVioletRed", "slateblue"] if ngroup == 2 - return colorbrewer.Set1[ngroup] if ngroup <= 9 - return d3.scale.category20().range()[0...ngroup] - else - return ["#bebebe"] if ngroup == 1 - return ["lightpink", "lightblue"] if ngroup == 2 - return colorbrewer.Pastel1[ngroup] if ngroup <= 9 - # below is rough attempt to make _big_ pastel palette - return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", - "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", - "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", - "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", - "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"][0...ngroup] - -# expand element/array (e.g., of colors) to a given length -# single elment -> array, then repeated to length n -expand2vector = (input, n) -> - return input unless input? # return null if null - return input if Array.isArray(input) and input.length >= n - input = [input] unless Array.isArray(input) - input = (input[0] for i of d3.range(n)) if input.length == 1 and n > 1 - input - -# median of a vector -median = (x) -> - return null if !x? - n = x.length - x.sort((a,b) -> a-b) - if n % 2 == 1 - return x[(n-1)/2] - (x[n/2] + x[(n/2)-1])/2 - -# given a vector of x's, return hash with values to left and right, and the differences -getLeftRight = (x) -> - n = x.length - x.sort( (a,b) -> a-b ) - - xdif = [] - result = {} - for v in x - result[v] = {} - - for i in [1...n] - #console.log("result:", result) - xdif.push(x[i]-x[i-1]) - result[x[i]].left = x[i-1] - for i in [0...(n-1)] - result[x[i]].right = x[i+1] - - xdif = median(xdif) - result.mediandiff = xdif - - result[x[0]].left = x[0]-xdif - result[x[n-1]].right = x[n-1]+xdif - result.extent = [x[0]-xdif/2, x[n-1]+xdif/2] - - result - -# maximum difference between adjacent values in a vector -maxdiff = (x) -> - return null if x.length < 2 - result = x[1] - x[0] - return result if x.length < 3 - for i in [2...x.length] - d = x[i] - x[i-1] - result = d if d > result - result - -# matrix extent, min max -matrixMin = (mat) -> - result = mat[0][0] - for i of mat - for j of mat[i] - result = mat[i][j] if result > mat[i][j] - result - -matrixMax = (mat) -> - result = mat[0][0] - for i of mat - for j of mat[i] - result = mat[i][j] if result < mat[i][j] - result - -matrixMaxAbs = (mat) -> - result = Math.abs(mat[0][0]) - for i of mat - for j of mat[i] - result = Math.abs(mat[i][j]) if result < mat[i][j] - result - -matrixExtent = (mat) -> [matrixMin(mat), matrixMax(mat)] - -d3.selection.prototype.moveToFront = () -> - this.each () -> this.parentNode.appendChild(this) - -d3.selection.prototype.moveToBack = () -> - this.each () -> - firstChild = this.parentNode.firstchild - this.parentNode.insertBefore(this, firstChild) if firstChild - -forceAsArray = (x) -> - return x unless x? # if null, return null - return x if Array.isArray(x) - [x] - -# any values in vec that appear in missing are made null -missing2null = (vec, missingvalues=['NA', '']) -> - vec.map (value) -> if missingvalues.indexOf(value) > -1 then null else value - -# display error at top of page -displayError = (message) -> - if d3.select("div.error").empty() # no errors yet - d3.select("body") - .insert("div", ":first-child") - .attr("class", "error") - d3.select("div.error") - .append("p") - .text(message) - -# sum values in an array -sumArray = (vec) -> (vec.reduce (a,b) -> a+b) - -# calculate cross-tabulation -calc_crosstab = (data) -> - nrow = data.ycat.length - ncol = data.xcat.length - - result = ((0 for col in [0..ncol]) for row in [0..nrow]) # matrix of 0's - - # count things up - for i of data.x - result[data.y[i]][data.x[i]] += 1 - - # row and column sums - rs = rowSums(result) - cs = colSums(result) - - # fill in column sums - for i in [0...ncol] - result[nrow][i] = cs[i] - - # fill in row sums - for i in [0...nrow] - result[i][ncol] = rs[i] - - # fill in total - result[nrow][ncol] = sumArray(rs) - - result - -# rowSums: the sums for each row -rowSums = (mat) -> (sumArray(x) for x in mat) - -# transpose: matrix transpose -transpose = (mat) -> ((mat[i][j] for i in [0...mat.length]) for j in [0...mat[0].length]) - -# colSums = the sums for each column -colSums = (mat) -> rowSums(transpose(mat)) - -# log base 2 -log2 = (x) -> - return(x) unless x? - Math.log(x)/Math.log(2.0) - -# log base 10 -log10 = (x) -> - return(x) unless x? - Math.log(x)/Math.log(10.0) - -# absolute value, preserving nulls -abs = (x) -> - return(x) unless x? +# A variety of utility functions used by the different panel functions + +# determine rounding of axis labels +formatAxis = (d, extra_digits=0) -> + d = d[1] - d[0] + ndig = Math.floor( Math.log(d % 10) / Math.log(10) ) + ndig = 0 if ndig > 0 + ndig = Math.abs(ndig) + extra_digits + d3.format(".#{ndig}f") + +# unique values of array (ignore nulls) +unique = (x) -> + output = {} + output[v] = v for v in x when v + output[v] for v of output + +# Pull out a variable (column) from a two-dimensional array +pullVarAsArray = (data, variable) -> + v = [] + for i of data + v = v.concat data[i][variable] + v + + +# reorganize lod/pos by chromosome +# lodvarname==null -> case for multiple LOD columns (lodheatmap) +# lodvarname provided -> case for one LOD column (lodchart) +reorgLodData = (data, lodvarname=null) -> + data.posByChr = {} + data.lodByChr = {} + + for chr,i in data.chrnames + #console.log("chr:", chr) + data.posByChr[chr[0]] = [] + data.lodByChr[chr[0]] = [] + for pos, j in data.pos + if data.chr[j].toString() == chr[0] + #console.log(data.chr[j] + " AND " + chr[0]) + data.posByChr[chr[0]].push(pos) + data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames) + lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) + data.lodByChr[chr[0]].push(lodval) + + #console.log("data.posByChr:", data.posByChr) + + if lodvarname? + data.markers = [] + for marker,i in data.markernames + if marker != "" + data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]}) + + data + +# calculate chromosome start/end + scales, for heat map +chrscales = (data, width, chrGap, leftMargin, pad4heatmap) -> + # start and end of chromosome positions + chrStart = [] + chrEnd = [] + chrLength = [] + totalChrLength = 0 + maxd = 0 + for chr in data.chrnames + d = maxdiff(data.posByChr[chr[0]]) + maxd = d if d > maxd + + rng = d3.extent(data.posByChr[chr[0]]) + chrStart.push(rng[0]) + chrEnd.push(rng[1]) + L = rng[1] - rng[0] + chrLength.push(L) + totalChrLength += L + + # adjust lengths for heatmap + if pad4heatmap + data.recwidth = maxd + chrStart = chrStart.map (x) -> x-maxd/2 + chrEnd = chrEnd.map (x) -> x+maxd/2 + chrLength = chrLength.map (x) -> x+maxd + totalChrLength += (chrLength.length*maxd) + + # break up x axis into chromosomes by length, with gaps + data.chrStart = [] + data.chrEnd = [] + cur = leftMargin + cur += chrGap/2 unless pad4heatmap + data.xscale = {} + for chr,i in data.chrnames + data.chrStart.push(cur) + w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i]) + data.chrEnd.push(cur + w) + cur = data.chrEnd[i] + chrGap + # x-axis scales, by chromosome + data.xscale[chr[0]] = d3.scale.linear() + .domain([chrStart[i], chrEnd[i]]) + .range([data.chrStart[i], data.chrEnd[i]]) + + # return data with new stuff added + data + + +# reorganize lod/pos by chromosome +# lodvarname==null -> case for multiple LOD columns (lodheatmap) +# lodvarname provided -> case for one LOD column (lodchart) +#reorgLodData = (data, lodvarname=null) -> +# data.posByChr = {} +# data.lodByChr = {} +# +# #console.log("data.chr", data.chr) +# #console.log("data.chrnames:", data.chrnames) +# the_chr = "0" +# for chr,i in data.chrnames +# data.posByChr[chr] = [] +# data.lodByChr[chr] = [] +# for pos,j in data.pos +# console.log("data.chr[j][0]:", data.chr[j][0]) +# if data.chr[j][0] == chr +# console.log("IS EQUAL") +# data.posByChr[chr].push(pos) +# data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames) +# lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames) +# data.lodByChr[chr].push(lodval) +# +# if lodvarname? +# data.markers = [] +# for marker,i in data.markernames +# if marker != "" +# data.markers.push({name:marker, chr:data.chr[i][0], pos:data.pos[i], lod:data[lodvarname][i]}) +# +# data + +# calculate chromosome start/end + scales, for heat map +#chrscales = (data, width, chrGap, leftMargin, pad4heatmap) -> +# # start and end of chromosome positions +# chrStart = [] +# chrEnd = [] +# chrLength = [] +# totalChrLength = 0 +# maxd = 0 +# for chr in data.chrnames +# d = maxdiff(data.posByChr[chr]) +# maxd = d if d > maxd +# +# rng = d3.extent(data.posByChr[chr]) +# chrStart.push(rng[0]) +# chrEnd.push(rng[1]) +# L = rng[1] - rng[0] +# chrLength.push(L) +# totalChrLength += L +# +# # adjust lengths for heatmap +# if pad4heatmap +# data.recwidth = maxd +# chrStart = chrStart.map (x) -> x-maxd/2 +# chrEnd = chrEnd.map (x) -> x+maxd/2 +# chrLength = chrLength.map (x) -> x+maxd +# totalChrLength += (chrLength.length*maxd) +# +# # break up x axis into chromosomes by length, with gaps +# data.chrStart = [] +# data.chrEnd = [] +# cur = leftMargin +# cur += chrGap/2 unless pad4heatmap +# data.xscale = {} +# for chr,i in data.chrnames +# data.chrStart.push(cur) +# w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i]) +# data.chrEnd.push(cur + w) +# cur = data.chrEnd[i] + chrGap +# # x-axis scales, by chromosome +# data.xscale[chr] = d3.scale.linear() +# .domain([chrStart[i], chrEnd[i]]) +# .range([data.chrStart[i], data.chrEnd[i]]) +# +# # return data with new stuff added +# data + +# Select a set of categorical colors +# ngroup is positive integer +# palette = "dark" or "pastel" +selectGroupColors = (ngroup, palette) -> + return [] if ngroup == 0 + + if palette == "dark" + return ["slateblue"] if ngroup == 1 + return ["MediumVioletRed", "slateblue"] if ngroup == 2 + return colorbrewer.Set1[ngroup] if ngroup <= 9 + return d3.scale.category20().range()[0...ngroup] + else + return ["#bebebe"] if ngroup == 1 + return ["lightpink", "lightblue"] if ngroup == 2 + return colorbrewer.Pastel1[ngroup] if ngroup <= 9 + # below is rough attempt to make _big_ pastel palette + return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", + "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", + "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", + "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", + "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"][0...ngroup] + +# expand element/array (e.g., of colors) to a given length +# single elment -> array, then repeated to length n +expand2vector = (input, n) -> + return input unless input? # return null if null + return input if Array.isArray(input) and input.length >= n + input = [input] unless Array.isArray(input) + input = (input[0] for i of d3.range(n)) if input.length == 1 and n > 1 + input + +# median of a vector +median = (x) -> + return null if !x? + n = x.length + x.sort((a,b) -> a-b) + if n % 2 == 1 + return x[(n-1)/2] + (x[n/2] + x[(n/2)-1])/2 + +# given a vector of x's, return hash with values to left and right, and the differences +getLeftRight = (x) -> + n = x.length + x.sort( (a,b) -> a-b ) + + xdif = [] + result = {} + for v in x + result[v] = {} + + for i in [1...n] + #console.log("result:", result) + xdif.push(x[i]-x[i-1]) + result[x[i]].left = x[i-1] + for i in [0...(n-1)] + result[x[i]].right = x[i+1] + + xdif = median(xdif) + result.mediandiff = xdif + + result[x[0]].left = x[0]-xdif + result[x[n-1]].right = x[n-1]+xdif + result.extent = [x[0]-xdif/2, x[n-1]+xdif/2] + + result + +# maximum difference between adjacent values in a vector +maxdiff = (x) -> + return null if x.length < 2 + result = x[1] - x[0] + return result if x.length < 3 + for i in [2...x.length] + d = x[i] - x[i-1] + result = d if d > result + result + +# matrix extent, min max +matrixMin = (mat) -> + result = mat[0][0] + for i of mat + for j of mat[i] + result = mat[i][j] if result > mat[i][j] + result + +matrixMax = (mat) -> + result = mat[0][0] + for i of mat + for j of mat[i] + result = mat[i][j] if result < mat[i][j] + result + +matrixMaxAbs = (mat) -> + result = Math.abs(mat[0][0]) + for i of mat + for j of mat[i] + result = Math.abs(mat[i][j]) if result < mat[i][j] + result + +matrixExtent = (mat) -> [matrixMin(mat), matrixMax(mat)] + +d3.selection.prototype.moveToFront = () -> + this.each () -> this.parentNode.appendChild(this) + +d3.selection.prototype.moveToBack = () -> + this.each () -> + firstChild = this.parentNode.firstchild + this.parentNode.insertBefore(this, firstChild) if firstChild + +forceAsArray = (x) -> + return x unless x? # if null, return null + return x if Array.isArray(x) + [x] + +# any values in vec that appear in missing are made null +missing2null = (vec, missingvalues=['NA', '']) -> + vec.map (value) -> if missingvalues.indexOf(value) > -1 then null else value + +# display error at top of page +displayError = (message) -> + if d3.select("div.error").empty() # no errors yet + d3.select("body") + .insert("div", ":first-child") + .attr("class", "error") + d3.select("div.error") + .append("p") + .text(message) + +# sum values in an array +sumArray = (vec) -> (vec.reduce (a,b) -> a+b) + +# calculate cross-tabulation +calc_crosstab = (data) -> + nrow = data.ycat.length + ncol = data.xcat.length + + result = ((0 for col in [0..ncol]) for row in [0..nrow]) # matrix of 0's + + # count things up + for i of data.x + result[data.y[i]][data.x[i]] += 1 + + # row and column sums + rs = rowSums(result) + cs = colSums(result) + + # fill in column sums + for i in [0...ncol] + result[nrow][i] = cs[i] + + # fill in row sums + for i in [0...nrow] + result[i][ncol] = rs[i] + + # fill in total + result[nrow][ncol] = sumArray(rs) + + result + +# rowSums: the sums for each row +rowSums = (mat) -> (sumArray(x) for x in mat) + +# transpose: matrix transpose +transpose = (mat) -> ((mat[i][j] for i in [0...mat.length]) for j in [0...mat[0].length]) + +# colSums = the sums for each column +colSums = (mat) -> rowSums(transpose(mat)) + +# log base 2 +log2 = (x) -> + return(x) unless x? + Math.log(x)/Math.log(2.0) + +# log base 10 +log10 = (x) -> + return(x) unless x? + Math.log(x)/Math.log(10.0) + +# absolute value, preserving nulls +abs = (x) -> + return(x) unless x? Math.abs(x) \ No newline at end of file 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 8d56d04b..8b73b85d 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee @@ -134,7 +134,7 @@ $('input[name=display_all]').change(() => ) $("#pylmm_compute").click(() => - $("#progress_bar_container").modal() + $("#progress_bar_container").modal({show:true}) url = "/marker_regression" $('input[name=method]').val("pylmm") $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val()) 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 e1ef8b63..92d3183a 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -132,7 +132,9 @@ $('input[name=display_all]').change((function(_this) { $("#pylmm_compute").click((function(_this) { return function() { var form_data, url; - $("#progress_bar_container").modal(); + $("#progress_bar_container").modal({ + show: true + }); url = "/marker_regression"; $('input[name=method]').val("pylmm"); $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val()); diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 29fa0469..e032dfc5 100755 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -72,7 +72,7 @@ -
+
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 277acffa..fcaabce3 100755 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -226,8 +226,8 @@
-
- +
+
@@ -242,12 +242,18 @@ +
- - - - - +
+ +
+
+ +
+
+ +
+
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html index 4e308c75..3378846a 100755 --- a/wqflask/wqflask/templates/new_security/login_user.html +++ b/wqflask/wqflask/templates/new_security/login_user.html @@ -26,21 +26,18 @@ -
-
- - -
- -
+ +
+
+ +
-
- -
+
+ +

Forgot your password?
@@ -48,22 +45,21 @@
-
-
+
+ +
+
- -
-
+
+ +
-
- -
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index af606600..5d0437df 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -18,13 +18,13 @@ -
- {% for key in hddn %} - - {% endfor %} -
+
+ {% for key in hddn %} + + {% endfor %} +
- +
@@ -81,18 +81,19 @@

- + Review and Edit Data

-
+
{% include 'show_trait_edit_data.html' %}
+ {% include 'show_trait_progress_bar.html' %}
@@ -134,7 +135,7 @@ - + {% endblock %} diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 88fd74d9..0afac1f7 100755 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -19,11 +19,11 @@ BLAT Specifity -
{{ "%s" % (this_trait.probe_set_specificity) }}
+
{{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}
{% endif %} {% if this_trait.probe_set_blat_score %}
BLAT Score
-
{{ "%s" % (this_trait.probe_set_blat_score) }}
+
{{ "%0.3f" | format(this_trait.probe_set_blat_score|float) }}
{% endif %} diff --git a/wqflask/wqflask/templates/show_trait_progress_bar.html b/wqflask/wqflask/templates/show_trait_progress_bar.html index aebf64a4..99906338 100755 --- a/wqflask/wqflask/templates/show_trait_progress_bar.html +++ b/wqflask/wqflask/templates/show_trait_progress_bar.html @@ -1,17 +1,40 @@ -