# HG changeset patch # User ethevenot # Date 1470500295 14400 # Node ID db1d80e89156178dff6c91363767191b4c78c65a # Parent ad06aeed02c99f76d21e96b23b019d5857417134 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 29f9ccf5bd558becff5913528bb998aa7bb82d44 diff -r ad06aeed02c9 -r db1d80e89156 README.md --- a/README.md Tue Aug 02 06:26:41 2016 -0400 +++ b/README.md Sat Aug 06 12:18:15 2016 -0400 @@ -1,12 +1,14 @@ -## Heatmap of the data matrix -#### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project +Heatmap of the data matrix +========================== + +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/heatmap.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/heatmap). ### Description -**Version:** 2.2.0 -**Date:** 2016-07-30 +**Version:** 2.2.2 +**Date:** 2016-08-04 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) **Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354) @@ -16,45 +18,52 @@ ### Installation -* Configuration file: **heatmap_config.xml** +* Configuration file: `heatmap_config.xml` * Image files: - + **static/images/heatmap_workflowPositionImage.png** - + **static/images/heatmap_workingExampleImage.png** -* Wrapper file: **heatmap_wrapper.R** + + `static/images/heatmap_workflowPositionImage.png` + + `static/images/heatmap_workingExampleImage.png` +* Wrapper file: `heatmap_wrapper.R` * R packages - + **batch** from CRAN -> install.packages("batch", dep=TRUE) + + **batch** from CRAN + + ```r + install.packages("batch", dep=TRUE) + ``` ### Tests -The code in the wrapper can be tested by running the **tests/heatmap_tests.R** in R +The code in the wrapper can be tested by running the `runit/heatmap_runtests.R` R file + +### Working example + +See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) -### News +### News + +##### CHANGES IN VERSION 2.2.2 + +INTERNAL MODIFICATION + + * Minor internal modifications ##### CHANGES IN VERSION 2.2.0 NEW FEATURES - o Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters) - - o The 1-abs(correlation) dissimilarity is now available (in addition to the default '1-correlation') in case the sign of correlations between samples and between variables does not matter, as well as the euclidean, maximum, manhattan, canberra, binary, and minkowski dissimilarities + * Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters) - o A new red-green color scale is available + * The 1-abs(correlation) dissimilarity is now available (in addition to the default '1-correlation') in case the sign of correlations between samples and between variables does not matter, as well as the euclidean, maximum, manhattan, canberra, binary, and minkowski dissimilarities -*** - + * A new red-green color scale is available + ##### CHANGES IN VERSION 2.1.2 INTERNAL MODIFICATION - o Creating additional files for planemo and travis validation + * Creating additional files for planemo and travis validation -*** - ##### CHANGES IN VERSION 2.0.2 INTERNAL MODIFICATION - o Creating tests for R code - -*** \ No newline at end of file + * Creating tests for R code \ No newline at end of file diff -r ad06aeed02c9 -r db1d80e89156 heatmap_config.xml --- a/heatmap_config.xml Tue Aug 02 06:26:41 2016 -0400 +++ b/heatmap_config.xml Sat Aug 06 12:18:15 2016 -0400 @@ -1,13 +1,18 @@ - + Heatmap of the dataMatrix R r-batch - + + + + + + @Manual{, + title = {R: A Language and Environment for Statistical Computing}, + author = {{R Core Team}}, + organization = {R Foundation for Statistical Computing}, + address = {Vienna, Austria}, + year = {2016}, + url = {https://www.R-project.org/}, + } @Article{Thevenot2015, Title = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses}, Author = {Thevenot, Etienne A. and Roux, Aurelie and Xu, Ying and Ezan, Eric and Junot, Christophe}, @@ -339,7 +361,8 @@ Doi = {10.1021/acs.jproteome.5b00354}, Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354} - } + } + 10.1093/bioinformatics/btu813 diff -r ad06aeed02c9 -r db1d80e89156 runit/exa1/dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/exa1/dataMatrix.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,39 @@ +dataMatrix S1 S2 S3 S4 S5 S6 +V1 196502 237810 198284 182894 105331 132150 +V2 2544571 2614302 2451909 3142179 3768416 3713752 +V3 1230784 1161975 1143745 1150915 1344578 1220503 +V4 1630089 1818363 1563465 2387030 3502620 2954208 +V5 2184963 2374515 1974647 2313226 1782744 1860757 +V6 5262172 6365930 5010369 9109487 6410977 6378638 +V7 2232587 2745906 2200995 3832216 2708070 2869295 +V8 483320 660332 433486 1062013 677822 748514 +V9 112905 136174 123604 162138 240686 195271 +V10 179154 195001 180519 98623 132470 123032 +V11 175220 169515 158401 111215 103539 159727 +V12 46503 55313 76310 46932 92318 43629 +V13 113796 91557 95960 92685 140973 112898 +V14 540798 596737 511783 876548 1626199 1385367 +V15 140806 135469 145016 229518 434119 398941 +V16 1334798 1318651 1308783 2345055 4068874 3565724 +V17 1083792 1145232 916864 838363 1678307 1304234 +V18 91671 101007 79999 85402 146939 126314 +V19 274181 282331 292645 394175 330817 293481 +V20 879658 809068 903330 1273966 959314 938277 +V21 608434 662366 727426 920178 1106194 1201520 +V22 1600960 1545158 1608816 1880288 2246189 2069613 +V23 2171614 2239769 2106004 2565354 4913676 4072322 +V24 4045143 3862213 4053630 7352540 5574415 6185035 +V25 202805 182042 165499 57267 86611 89320 +V26 586997 667911 522193 748212 595063 659353 +V27 229790 256287 253497 1189248 1025521 746948 +V28 1644853 1759382 1760494 3379214 4572430 4386799 +V29 8491372 9275641 8655578 12105700 13265172 13484917 +V30 724039 730730 640992 1475658 1191085 1213210 +V31 86524840 89500400 88593487 183705591 150949959 169189091 +V32 26916143 30167854 28256416 39049936 45546213 47237473 +V33 2683733 2654918 2386486 4786536 3622659 3879731 +V34 3919797 4529379 3595989 7965534 5963667 6339219 +V35 84384696 90691983 83322980 51888441 86013709 79735533 +V36 95751916 101056674 92760886 129551865 109580811 118980909 +V37 374328 416298 355931 255675 371223 338701 +V38 2219529 2333885 2206832 903780 981633 1136522 diff -r ad06aeed02c9 -r db1d80e89156 runit/exa1/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/exa1/sampleMetadata.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,7 @@ +sampleMetadata smeta1 smeta2 +S1 196502 2544571 +S2 237810 2614302 +S3 198284 2451909 +S4 182894 3142179 +S5 105331 3768416 +S6 132150 3713752 diff -r ad06aeed02c9 -r db1d80e89156 runit/exa1/variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/exa1/variableMetadata.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,39 @@ +variableMetadata vmeta1 vmeta2 vmeta3 vmeta4 vmeta5 vmeta6 +V1 196502 237810 198284 182894 105331 132150 +V2 2544571 2614302 2451909 3142179 3768416 3713752 +V3 1230784 1161975 1143745 1150915 1344578 1220503 +V4 1630089 1818363 1563465 2387030 3502620 2954208 +V5 2184963 2374515 1974647 2313226 1782744 1860757 +V6 5262172 6365930 5010369 9109487 6410977 6378638 +V7 2232587 2745906 2200995 3832216 2708070 2869295 +V8 483320 660332 433486 1062013 677822 748514 +V9 112905 136174 123604 162138 240686 195271 +V10 179154 195001 180519 98623 132470 123032 +V11 175220 169515 158401 111215 103539 159727 +V12 46503 55313 76310 46932 92318 43629 +V13 113796 91557 95960 92685 140973 112898 +V14 540798 596737 511783 876548 1626199 1385367 +V15 140806 135469 145016 229518 434119 398941 +V16 1334798 1318651 1308783 2345055 4068874 3565724 +V17 1083792 1145232 916864 838363 1678307 1304234 +V18 91671 101007 79999 85402 146939 126314 +V19 274181 282331 292645 394175 330817 293481 +V20 879658 809068 903330 1273966 959314 938277 +V21 608434 662366 727426 920178 1106194 1201520 +V22 1600960 1545158 1608816 1880288 2246189 2069613 +V23 2171614 2239769 2106004 2565354 4913676 4072322 +V24 4045143 3862213 4053630 7352540 5574415 6185035 +V25 202805 182042 165499 57267 86611 89320 +V26 586997 667911 522193 748212 595063 659353 +V27 229790 256287 253497 1189248 1025521 746948 +V28 1644853 1759382 1760494 3379214 4572430 4386799 +V29 8491372 9275641 8655578 12105700 13265172 13484917 +V30 724039 730730 640992 1475658 1191085 1213210 +V31 86524840 89500400 88593487 183705591 150949959 169189091 +V32 26916143 30167854 28256416 39049936 45546213 47237473 +V33 2683733 2654918 2386486 4786536 3622659 3879731 +V34 3919797 4529379 3595989 7965534 5963667 6339219 +V35 84384696 90691983 83322980 51888441 86013709 79735533 +V36 95751916 101056674 92760886 129551865 109580811 118980909 +V37 374328 416298 355931 255675 371223 338701 +V38 2219529 2333885 2206832 903780 981633 1136522 diff -r ad06aeed02c9 -r db1d80e89156 runit/exa2/dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/exa2/dataMatrix.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,117 @@ +dataMatrix S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15 S16 S17 S18 S19 S20 S21 S22 S23 S24 S25 S26 S27 S28 +V1 1484.78 1106.3 1217.84 1441.38 1213.63 1302.49 1412.79 1322.28 1258.89 1365.49 1146.78 1243 1242.47 1250.61 1307.52 1423.59 1290.51 1126.64 1421.23 1235.75 1084.56 1252.87 1254.74 1584.64 1474.43 1283.85 1347.74 1557.35 +V2 0 0 0 13.14 0 0 0 16.36 0 0 11.8 0 0 0 0 12.34 12.45 0 0 6.87 6.41 0 15.53 12.87 0 14.58 0 0 +V3 0 5.93 7.82 16.41 7.58 9.54 8.25 20.52 5.89 6.27 20.86 5.2 8.97 10.93 6.51 21.06 25.05 0 0 11.79 16.97 7.23 19.58 20.56 11.07 20.87 0 6.18 +V4 10.86 12.56 7.93 14.32 10.64 11.38 8.24 15.8 11.75 11.29 12 6.34 8.05 16.12 13.33 18.81 24.44 8.26 6.99 9.76 10.29 9.11 19.32 26.55 15.58 17.38 3.31 7.2 +V5 9.49 5.72 6.96 5.48 6.38 9.57 6.31 8.67 8.21 9.1 9.23 9.68 7.1 6.89 4.39 7.98 11.58 7.71 10.99 8.67 13.18 7.19 10.96 5.86 7.98 10.39 4.69 11.78 +V6 43.5 19.95 34.96 31.98 31.27 49.9 38.17 26.44 27.19 40.64 40.9 47 26.26 30.31 20.64 49.54 49.06 26.73 64.56 43.29 80.61 38.08 42.01 37.22 26.37 25.97 25.2 41.05 +V7 333.79 311.77 321.24 391.51 297.03 263.85 246.39 221.76 447.49 418.79 300.37 414.43 262.68 244.09 213.24 423.97 523.16 344.76 413.98 402.45 251.38 225.47 300.48 230.58 301.51 246.9 361.04 375.51 +V8 49.48 20.81 27.33 17.44 15.39 14.84 17.67 13.41 29.27 63.13 34.04 23.41 25.16 16.2 11.68 42.53 31.46 12.83 38.02 40.28 25.77 12.44 41.05 15.25 23.21 27.11 25.98 22.33 +V9 2.56 1.18 1.07 1.39 2.59 2.53 1.98 3.84 1.61 1.72 1.76 1.73 0.63 2.13 2.02 2.44 0 1.24 1.22 1.87 7.83 4.15 5.88 4.77 5.77 7.81 0 1.67 +V10 6.37 4.55 2.63 5.09 6.29 6.32 6.31 6.61 4.35 5.98 4.79 6.3 1.24 6.98 5.09 6.64 7.21 3.63 4.14 5.47 19.45 8.4 9.41 10.83 10.78 11.98 1.29 3.86 +V11 11.9 21.21 10.67 19.08 17.84 10.64 13.61 10.41 17.75 17.87 13.24 15.27 7.83 18.66 13.5 18.67 26.37 14.46 13.18 18.29 26.21 10.65 16.46 21.52 19.57 17.89 8.81 10.4 +V12 4.38 8.56 4.95 8.83 5.87 3.53 5.15 0.45 7.67 5.85 5.32 4.88 4.55 5.87 5.12 6.16 10.97 6.67 4.69 6.11 7.33 3.34 5.44 8.94 5.83 5.07 5.77 3.8 +V13 0.78 1.17 0.61 1.21 0.89 0 0.56 0.45 1.04 1.03 0 0.71 0.62 0.78 0 1.25 0 0.63 1.1 1.16 1.13 0 0.87 1.05 1.06 0.63 0.36 0.82 +V14 1511.11 1158.59 1529.32 1471.39 1654.17 2320.94 2630.11 2148.49 1248.21 1590.03 1120.83 1388.4 1523.12 2293.02 0 1566.36 1543.42 842.31 1421.66 1850.9 2870.84 2338.83 1979.28 3581.78 1757.49 2983.66 2967.62 1392.97 +V15 638.35 560.78 803.6 597.71 719.25 805.09 773.49 777.4 566.6 780.02 607.71 493.24 655.73 880.88 0 768.64 625.98 451.52 443.79 745.64 692.9 839.58 727.49 1376.26 622.72 1421.07 997.77 827.06 +V16 165.37 51.55 130.59 57.95 98.46 310.56 233.32 147.43 39.69 109.04 0 101.57 0 97.94 0 107.15 90.92 0 177.32 137.54 432.77 267.66 128.29 331.03 144.05 118.52 162.61 64.33 +V17 1586.23 2103.69 1926.52 1614.01 2166.04 2284.19 2506.01 2040.02 1327.06 1705.97 1461.31 1649.21 1759.17 2442.95 0 1875.52 1881.42 1512.88 1520.67 1981.82 3021.6 2389.78 2088.67 4697.26 1646.11 3269.32 2805.59 2315.4 +V18 243.32 227.33 349.71 195.5 327.78 307.89 703.12 197.9 0 234.07 330.09 246.26 256.2 419.19 0 265.17 192.4 188.52 255.13 481.91 462.41 216.66 336.29 478.85 152.09 424.2 257.62 198.53 +V19 1921.6 2015.61 2872.21 2975.67 2406.07 2438.08 2381.42 2789.98 2881.8 2119.69 1953.23 1880.63 1985.58 1819.19 0 2343.84 2473.67 1909.11 1798.62 2824.34 1735 2429.73 1958.41 4299.39 2609.31 3374.62 2824.95 3079.01 +V20 539.06 432.85 724.98 347.76 380.87 522.5 444.07 550.04 502.86 576.95 744.34 410.58 415.64 321.36 0 805.68 451.18 292.67 471.68 793.63 804.05 679.41 0 1047.85 444.04 444.5 547.87 738.82 +V21 288.7 0 0 0 0 0 0 0 0 144.5 0 0 0 154.85 0 119.48 0 0 0 0 0 0 0 179.2 0 208.44 0 0 +V22 273.95 149.66 287.92 0 327.34 0 717.56 0 0 311.8 0 121.95 0 172.76 0 238.66 161.38 0 0 0 0 0 608.86 398.84 173.3 462.34 347.64 312.02 +V23 614.701 98.849 0 217.085 320.044 246.769 107.187 114.252 185.453 0 0 179.589 0 0 0 169.996 58.781 133.231 209.81 106.94 159.654 97.758 160.071 0 131.035 0 169.996 0 +V24 7.329 7.035 6.437 5.973 6.656 0 0 6.663 7.697 7.511 6.876 7.531 6.817 6.579 5.978 0 7.191 7.57 6.105 6.994 6.84 0 0 0 7.322 7.182 0 5.935 +V25 28.846 26.604 26.246 0 25.943 0 24.929 0 29.452 27.652 28.324 28.299 0 0 24.957 0 28.278 28.029 25.955 27.292 27.437 24.795 0 0 0 26.468 0 0 +V26 16.71 15.574 15.343 0 0 14.629 0 16.021 18.624 16.703 16.82 15.859 15.086 14.725 14.543 0 16.698 16.782 14.461 16.186 16.36 0 0 14.682 0 14.853 0 14.503 +V27 187.78 134.86 104.51 164.53 145.23 101.57 194.53 143.99 147.12 34.35 110 105.84 95.85 160.24 97.8 108.21 112.99 23.83 110.36 146.6 127.22 132.54 134.6 123.13 156.39 138.56 133.67 14.17 +V28 20.22 14.96 11.79 17.94 16.79 11.55 22.08 17.8 16.64 3.74 13.56 12.82 11.43 19.05 11.62 12.97 13.58 2.8 13.44 17.3 15.87 14.87 16.1 14.06 16.01 17.45 15.64 1.43 +V29 75.78 77.98 38.21 69.93 86.6 35.94 93.92 70.68 68.63 21.05 45.99 55.4 45.65 58.75 39.82 34.02 46.6 9.28 29.73 65.55 65.73 62.13 56.75 35.83 61.46 60.77 54.74 13.94 +V30 12.75 14.38 8.06 13.79 15.45 7.33 16.09 14.9 12.84 3.34 8.78 11.42 9.47 12.32 7.87 7.82 9.61 1.87 8.15 11.43 13.59 8.63 11.36 8.74 10.62 15.01 10.94 2.45 +V31 152.24 143.82 99.08 127.98 140.79 77.54 137.85 112.09 123.92 25.64 107.74 112.76 89.79 107.46 71.99 82.81 95.43 16.35 78.04 79.82 132.59 126.74 133.86 82.86 109.23 124.44 108.45 24.55 +V32 938.99 725.51 504.85 599.76 701.02 393.83 668.81 533.32 633.26 165.95 562.51 557.52 415.33 598.74 338.85 352.62 470.93 115.55 385.39 327.2 589.46 648.36 743.1 360.36 591.98 574.85 527.59 150.99 +V33 2988.64 2781 2451.36 2290.88 2497.75 1772.76 2434.42 2222.88 2429.96 365.39 2071.07 2358.74 1919.88 2141.82 1236.79 1292.48 1836.8 465.52 1668.16 1167.73 2095.17 3286.45 2900.66 1323.11 2346.08 2245.29 2129.08 735.12 +V34 1644.27 1378.93 970.38 1310.7 1277.11 838.94 1276.17 1038.97 1216.93 256.38 1070.93 1248.62 908.78 1301.31 795.45 690.35 1002.58 246.43 1039.85 738.11 1609.77 1444.48 1417.84 843.04 1359.28 1512.42 1245.6 326.87 +V35 34.28 28.91 29.9 31.11 38.88 17.48 39.24 23.23 30.38 7.43 19.24 32.68 22.86 29.83 13.98 13.69 22.05 7.96 21.14 30.86 25.14 34.58 29.31 14.04 32.27 29.3 27.08 6.72 +V36 34.69 25.94 25.12 31.06 34.84 18.45 27.52 20.78 27.3 6.01 16.27 32.31 21.57 24.55 15.88 13.34 20.65 7.03 16.83 25.77 27.02 38.17 26.83 15.03 36.42 32.65 27.34 8.39 +V37 53.33 33.39 38.28 56 18.46 33.81 39.24 25.03 37.19 12.79 19.02 29.64 29.32 36.33 21.06 26.69 27.01 6.3 24.3 49.3 23.38 133.19 49.05 20.55 57.23 32.46 48.68 36.85 +V38 55.46 32.06 38.14 73.93 17.66 27.63 40.29 24.64 38.73 18.25 17.06 30.63 28.54 39.35 15.18 27.94 26.45 9.01 22.52 62.43 17.96 222 42.3 16.94 65.81 35.65 60.7 67.84 +V39 1615.79 832.94 948.85 1163.14 780.73 932.8 827.92 651.39 969.19 300.59 651.84 688.09 704.96 886.23 511.33 657.76 683.37 120.74 872.17 1307.25 802.54 2032.41 1544.2 758.36 1356.28 1432.05 1263.16 435.85 +V40 1699.27 766.05 997.32 1114.23 990.02 987.62 890.66 680.92 1015.76 309.1 716.86 590.9 623.14 866.72 485.55 674.31 659.58 128.63 766 948.5 764.57 1414.08 1579.67 769.54 1269.34 1677.86 1148.7 383.33 +V41 3995.34 1888.42 2393.66 1835.16 1684.97 1796.85 1192.55 1091.08 1984.75 909.69 1763.01 1285.69 1150.88 1126.86 1048.41 1193.59 1261.41 257.87 1437.84 1248.8 1395.5 2019.26 3393.17 1548.47 2189.84 2792.08 2003.12 761.04 +V42 6200.76 2703.73 3569.72 2967.38 2647.22 2701.52 1896.29 1731.65 3052.28 1397.8 2729.69 1770.64 1689.06 1813.5 1552.25 1977.75 1922.15 419.79 2262.29 1830.99 2226.75 2961.28 5042.17 2440.05 3329.37 4602.08 3086.87 1171.63 +V43 2766.76 1286.7 1535.67 1776.16 1043.65 1253.94 1165.85 989.89 1477.33 581.17 1081.96 962.62 1015.15 1217.68 877.56 1123.53 1046.42 120.87 1150.86 1405.41 1211.44 2590.33 1996.95 1466.31 2124.7 2561.89 1813.49 583.43 +V44 1808.56 1052.58 1064.38 1465.2 861.99 1062.52 1290.66 962.53 1196.05 311.32 811.08 1038.58 980.55 1253.84 820.41 794.37 949.8 179.67 766.54 1582.99 1107.43 3061.94 1384.89 1171.4 1849.11 2223.83 1643.52 731.04 +V45 361.49 289.55 263.82 424.39 250.66 201.69 240.88 240.95 284.18 73.44 248.27 273.46 216.48 217.64 165.11 174.49 215.91 41.61 227.97 327.36 274.12 615.76 379.63 251.66 345.47 506.13 366.01 133.46 +V46 2607.82 2000.16 1671.95 2357.94 1683.26 1571.32 1935.52 1840.49 1958.56 359.59 1995.27 1867.04 1691.03 1610.68 1121.25 1356.18 1606.91 323.82 1288.12 2384.86 1957.6 4620.77 2142.9 2097.88 2778.2 3638.56 2613.61 1057.86 +V47 4306.74 3278.54 2766.81 3676.12 2584.89 2707.8 3218.81 3013.78 3194.19 573.31 3189.42 3307.49 2902.72 2845.79 2162.9 2270.99 2779.88 470.14 2005.07 3846.66 3287.96 7678.68 3441.2 3648.6 4534.31 6234.27 4334.59 1807.15 +V48 2757.36 1972.09 1921.97 2047.43 2307.53 3450.36 2481.9 3192.32 2516.37 573.41 1605.23 4187.86 1340.3 2548.83 2241.75 1147.41 2178.56 1120.09 946.32 1988.3 3012.52 4348.05 4947.77 2894.49 2605.46 6227.79 3371.34 1704.39 +V49 2846.27 2112.17 2074.85 2484.04 2030.38 2892.38 2323.34 2689.36 2431.6 349.58 1659.98 3637.59 1615.48 2586.62 2360.5 1413.49 2212.28 835.81 1208.92 2272.05 2841.18 5130.58 4188 2879.36 2853.44 5754.18 3390.96 1517.17 +V50 63.24 68.39 44.94 64.93 37.36 31.18 60.74 35.49 50.78 15.1 52.13 43.34 53.45 55.07 31.66 31.25 44.48 10.88 33.05 60.72 34.37 209.37 55.71 37.41 51.12 69.22 68.87 58.26 +V51 1745.37 1185.09 1129.87 1082.42 1354.59 1492.4 1089.89 1391.1 1308.84 232.89 1028.07 1955.9 729.97 1004.49 961.76 574.74 1042.49 481.45 420.8 926.39 1134.46 2690.76 2585.95 984.56 1268.87 2558.63 1571.3 896.32 +V52 2325.89 1572.13 1488.2 1298.49 1823.74 2252.49 1456.85 2073.13 1786.37 391.59 1356.24 2938.31 868.29 1287.9 1431.16 730.25 1435.36 788.12 531.96 1115.79 1682.73 2924.65 3710.59 1520.02 1620.38 3734.6 2105.09 1202.01 +V53 352.51 261.05 248.74 309.45 289.73 416.53 266.85 428.71 321.69 70.28 236.94 537.25 193.5 326 319.28 189.21 300.36 130.33 152.84 203.76 442.22 511.73 516.04 437.43 331.36 880.17 434.44 225.04 +V54 216.14 119.32 400.57 336.36 56.47 89.37 155.36 49.48 177.88 130.48 97.22 114.95 135.48 117.64 76.58 160.44 117.05 29.18 83.99 83.8 18.56 195.87 181.22 21.21 196.54 152.66 116.73 74.64 +V55 3354.74 1889.02 3463.96 2595.51 1095.04 1188.43 1840.09 983.93 2051.34 989.95 1188.04 1824.94 1599.03 1844.36 1384.25 1654.65 1582.54 256.02 1244.41 1674.07 559.55 2535.71 2199.75 710.19 2034.19 3209.59 1770.93 909.24 +V56 689.37 323.77 632.5 615.72 142.49 199.66 291.67 166.84 382.75 226.87 180.91 296.75 246.47 305.63 207.47 338.53 262.63 61.25 203.85 288.31 71.53 584.03 353.14 107.89 389.42 519.26 314.68 183.74 +V57 6414.27 4067.65 4605.44 4227.56 3397.35 4016.57 3910.51 3544.13 4272.94 943.77 3394.68 4289.36 3906.95 4409.8 3951.68 4184.76 4022.87 363.34 3950.15 6095.62 3268.86 5116.94 4149.28 5007.15 4429.98 9674.53 5211.56 1994.81 +V58 6266.36 3952.06 4638.28 5920.74 2062.48 2497.54 4169.02 3215.66 4090.27 1503.58 1974.3 2964.15 3022.96 3735.08 2495.87 3708.52 2983.48 685.38 2577.02 5480.39 1887.75 9838.32 2801.7 2511.25 3945.65 6713.94 4469.5 2726.1 +V59 2080.03 874.53 1695.81 1374.04 1394.91 765.07 1135.71 1004.63 1290.59 440.83 1819.62 1091.7 968.82 881.98 936.64 1111.28 1135.01 347.02 942.22 791.46 436.14 1258.84 1124.31 632.85 885.87 2287.78 1044.93 565.34 +V60 4019.07 2882.43 2920.72 2773.03 2331.94 2583.34 2238.8 2947.54 2837.11 547.71 2278.86 2457.49 2253.88 2589.84 2426.05 2732.92 2456.51 183.15 2860.57 3738.87 2620.94 4076.27 2372.31 3116.74 2923.46 6850.52 3569.96 1439.67 +V61 30316.42 25360.24 24223.65 23154.87 18133.87 22307.77 23062.85 23590.21 23768.74 3389.17 15197.09 21838.91 19822.74 25644.43 20471.11 22104.93 20846.53 3426.18 25946.74 31472.14 23168.38 33432.4 20220.09 23962.44 22402.54 56752.04 29669.59 11842.22 +V62 62402.87 35366.22 42321.8 31258.28 45712.77 37769.84 37522.2 43278.66 41954.08 9480.21 43459.12 35791.78 33007.49 37555.87 30867.86 39466.54 36691.44 4528.68 42271.25 38040.41 33835.98 31348.66 36815.48 42979.08 35687.18 100505.6 45185.45 22694.47 +V63 5345.95 2464.9 3091.4 2805.39 3415.52 2539.93 3108.55 3202.34 3246.75 909.16 3585.55 2965.11 2611.3 2390.26 2831.05 3065.67 2908.16 412.12 2899.18 2910.75 2276.04 2502.17 3031.16 2991.49 2581.47 8752.35 3493.07 2141.79 +V64 5292.96 4008.72 4012.44 3886.04 3647.09 4488.47 3153.78 4115.83 4075.66 624.71 3329.53 3032.83 2312.02 3514.26 3087.36 3808.11 3180.69 512.3 5079.61 5010.13 3983.6 3431.06 4013.46 4214.52 3237.19 10957.47 4990.88 2498.27 +V65 25444.34 13558.49 16493.22 12642.32 18907.52 18009.06 14231.51 18620.1 17238.32 4086.37 19094.31 14715.79 12230.13 14978.12 11587.05 17803.28 15068.11 2966.33 20658.33 15965.36 15559.69 10040.91 15401.79 19709.15 13056.25 46168.25 19569.97 11265.33 +V66 13899.53 8944.63 10159.96 11074.5 10592.6 8214.08 10176.94 9842.82 10363.13 1692.08 10224.02 8347.23 9132.47 9222.4 7107.34 10746.74 9130.03 1305.62 12811.74 12563.23 8865.71 12920.36 8100.75 11165.92 10182.24 27260.68 12983.83 6047.39 +V67 23512.63 13724.09 15652.33 13277.44 14818.7 9962.66 15178.26 16531.8 15332.24 3861.68 16746.25 14037.72 17098.1 13131.82 11032.59 15239.5 14547.66 2299.46 12753.96 18982.74 12462.65 21193.96 9974.96 15787.58 16677.68 36925.01 18094.82 8438.68 +V68 821.85 585.07 674.53 840.2 718.19 574.86 651.98 653.13 689.98 98.6 706.95 560.39 503.06 591.94 388.25 697.71 574.72 120.85 1200.77 898.01 617.64 580.33 598.67 661.06 518.03 1915.59 873.76 476.91 +V69 5665.21 3978.35 4089.75 6323.17 5026.21 3349.48 4344.41 4708.65 4685.65 964.71 5080.09 3035.72 3840.01 3568.7 2368.7 4560.78 3742.33 988.46 7508.69 6081.63 3875.94 4956.96 3618.8 4029.91 4201.27 11407.44 5710.08 2652.15 +V70 22886.12 12566.47 13528.14 14763.84 14470.03 10368.79 13211.34 16198.81 14749.19 3707.08 18464.21 12968.59 14976.46 11752.16 9218.14 15570.81 13825.06 3229.53 15895.44 17072.56 12786.98 16896.42 8923.53 16188.56 14585.89 34726.7 17134.51 7604.44 +V71 11423.67 7260.23 8970.27 7850.77 7000.97 7015.29 6913.61 7283.92 7964.84 1553.03 6763.98 8126.89 6577.43 7492.23 8528.18 8010.27 7583.16 782.55 8054.41 8188.51 6660.61 8871.33 7225.66 8376.3 7110.27 20520.68 9375.97 4562.98 +V72 15637.27 10686.69 12884.29 7658.22 11941.71 16143.55 12067.08 13664.64 12585.43 2720.13 8240.99 12552.56 6342.23 11346.03 11072.08 8526.86 9680.13 2345.48 10280.75 9082.97 11453.12 8256.47 14972.26 12789.22 8817.57 34220.75 13734.14 8577.94 +V73 135.27 87.47 100.36 112.7 84.8 79.57 89.6 87.62 97.17 18.55 90.81 70.86 83.71 83.59 71.35 94.23 82.42 9.69 140.04 119.03 80.9 117.49 74.17 97.09 93.08 275.42 124.65 64.66 +V74 14754.19 9880.17 10295.05 8265.04 9657.1 14237.48 10965.97 14015.39 11508.8 2467.86 7500.76 12549.98 5789.86 8750.01 8146.62 7193.56 8321.8 2299.97 8467.08 8028.29 8820.04 6808.25 13820.28 11066.16 7654.05 27388.57 11506.59 6795.54 +V75 5044.67 4123.9 3380.68 3943.65 4810.8 3194.4 5781.71 4796.76 4384.57 880.42 3954.38 4991.5 3876.63 4266.2 4298.95 3072.12 4076.63 630.29 4034.2 4324.63 2909.16 3440.2 4620.79 2600.36 4008.27 5293.72 3903.92 890.76 +V76 27989.88 27031.11 27818.36 26202.32 31496.87 31500.9 29211.25 33237.97 29311.08 2502.57 30111.45 28276.59 27232.92 31880.59 26296.06 28183.17 28663.46 2023.76 31918.73 34538.92 29086.99 27914.54 27498.1 39484.04 33320.98 43351.62 33389.24 5645.12 +V77 6033.59 5638.84 5757.39 5676.17 6856.34 6971.39 5687.13 8714.58 6416.93 1072.27 6824.08 6173.48 5757.01 6766.91 5862.96 6737.69 6353.69 483.48 7038.06 7289.71 6550.93 6474.58 6456.35 8406.92 5959.81 9192.51 7171.11 1101.49 +V78 7531.71 9766.33 7917.05 7066.02 12533.47 8597.12 10418.97 11146.66 9372.17 1920.47 9102.5 9784.31 7945.3 9496.2 8096.37 6447.88 8478.76 1239.67 6847.86 10800.66 8877.01 9466.25 7931.75 8909.79 9603.09 8932.52 8921.12 1169.52 +V79 3370.7 4671.45 3614.71 3446.79 5356.27 4618.38 4037.77 7068.76 4523.1 1239.4 4406.1 4263.32 3463.28 4600.41 3959.76 3752.84 4074.29 427.18 3553.62 5079.92 4848.24 4350.41 4002.13 5329.31 3919.06 4823.83 4488.31 627.07 +V80 2868.85 5047.99 6140.96 3806.85 7216.89 5022.46 5256.06 7169.93 5316.25 1519.33 6397.22 6182.99 4471.19 4996.46 5044.24 3879.66 5161.96 972.74 4630.92 5302.12 5241.23 6062.4 4313.43 6004.09 4748.38 3915.5 5027.26 767.88 +V81 1281.17 2380.08 2630.57 1937.7 2948.17 2691.06 2049.1 4141.95 2507.47 842.56 2926.15 2622.13 1919.88 2621.26 2455.64 2368.02 2485.52 336.42 2351.46 2619.77 3160.6 2527.13 2012.54 3985.57 2068.56 2219.55 2618.15 662.38 +V82 2146.74 3932.04 7069.54 3549.09 7827.98 6430.48 4776.82 6935.8 5333.56 2022.04 6914.18 5835.39 4308.74 5546.11 4125.61 3316.45 5007.75 1321.86 5274.98 6382.23 4334.58 7275.77 4046.02 6099.75 5484.72 2524.77 5177.85 1504.1 +V83 1907.68 3559.05 5257.18 3193.54 6000.27 5750.61 3999.64 7589.13 4657.14 1824.28 6055.9 5410.81 3697.01 5334.87 4176.24 3397.35 4678.7 1069.69 5656.93 5396.48 4561.55 5252.67 3739.43 5920.38 4914.96 2876.17 4789.82 1031.33 +V84 1563.87 3853.97 8432.18 3998.8 8762.48 7300.71 5457.68 7690.55 5882.53 2579.31 7568.64 6990.02 4975.96 6365.79 4614.85 3298.13 5635.56 1615.25 6009.26 8596.72 5386.72 9056.14 3895.21 8087.23 6738.97 2065.6 6229.48 2415.73 +V85 3302.09 7922.23 14839.62 8695.1 14895.67 16252.17 9849.17 16439.95 11524.5 4784.86 15467.28 13457.69 9570.14 14436.95 11137.53 7751.42 11970.17 2992.62 14886.11 19383.47 13977.26 15573.95 8041.42 19837.99 14672.95 5478.44 13981.45 4998.55 +V86 0 296.05 366.33 1166.3 169.79 130.5 910.02 161.2 400.02 414.37 118.7 194.08 229.06 300.62 98.91 317.51 209.81 90.62 117.23 575.01 90.37 827.4 371.26 112.71 288.72 0 297.84 283.19 +V87 4401.04 2934.89 3681.01 6152.67 2603.61 2332.57 5978.46 1842.04 3740.79 1638.59 2181.44 2571.46 2344.9 3162.33 1741.34 4144.96 2691.07 852.26 2984.39 3569.27 1848.09 3728.68 4482.7 3372.3 3045.7 5581.86 3576.62 1103.72 +V88 4420.06 1904.34 2745.79 4347.63 2944.8 1893.85 4677.78 1650.45 3073.09 1248.88 2285.76 1717.32 1691.2 1981.19 1265.7 3952.21 2148.9 946 1923.49 2689.61 1150.01 2382.48 3544.16 2397.09 2072.07 4295.69 2556.82 977.41 +V89 2025.01 1309.69 1534.02 1724.7 997.37 1112.13 1504.17 1062.01 1408.64 356.9 1060.36 1233.53 1053.84 1231.26 1037.81 1653.63 1211.74 234.19 1373.49 870.32 1061.5 971.79 1322.44 1953.7 1160.28 3600.17 1539.21 897.22 +V90 7867.46 4397.17 5500.73 6128.55 4480.76 4361.83 6223.22 3656.82 5327.07 1374.86 5401.66 4479.81 3795.24 4545.42 3955.3 6335.78 4752.2 958.89 5860.18 3637.58 3601.16 3030.4 5119.26 7934.1 3942.76 12438.43 5695.48 3154 +V91 15420.21 6374.06 8675.69 9187.97 9400.76 7612.14 11663.12 6741.51 9384.43 2960.52 10596.69 7079.71 6181.61 7096.04 6025.42 12463.24 8240.45 2652.77 9551.32 5992.62 5097.49 4421.58 9300.09 12959.02 6316.93 21213.88 9356.62 5563.45 +V92 6810.22 3429.58 4299.33 6127.84 4075.32 3344.66 5125.32 3028.74 4530.12 1375.11 4175.7 3140.88 3084.36 3031.18 2636.89 6669.27 3789.71 1500.91 3604.49 2605.3 2145.3 2993.63 4287.71 5353.81 3153.44 9144.78 4161.06 2250.33 +V93 0 354.36 350.3 379.16 287.08 292.88 444.09 303.69 301.44 132.41 207.65 392.54 274.35 267.83 257.3 382.95 297.1 74.08 238.86 145.6 268.33 189 452.98 351.16 243.21 1063.47 369.08 296.38 +V94 2856.36 2456.4 2540.2 3367.98 2179.99 1475.83 2299.58 2163.25 2417.45 552.18 1869.28 2155.91 1924.65 1709.17 1633.53 3130.02 2070.43 550.12 1852.97 935.78 2010.54 1819.26 2184.75 2451.9 1909.68 5332.67 2312.19 1296.17 +V95 24091.97 15443.29 15942.72 17970 12145.72 10870.02 14682.71 15930 15884.55 4008.56 13247.25 15454.42 13712.53 11623.37 9969.61 19752.29 13959.91 3398.12 9621.47 5782.84 11913.08 12015.65 12566.22 17116.78 13006.74 34928.36 14618.89 8804.83 +V96 60793.4 33382.53 33715.73 32764.43 24127.78 25432.17 29776.84 35260.09 34406.62 11394.51 28888.49 34024.7 31279.19 25136.41 21490.99 42646.24 30577.67 7389.9 16961.84 12299.55 24074.2 26183.98 25604.38 38438.79 28979.32 78126.8 31333.61 20446.85 +V97 17570.51 9240.64 9721.88 10284.94 6788.15 7088.16 9220.42 9323.72 9904.8 3334.56 7668.14 9513.44 7976.91 7000.53 6579.27 12453.69 8532 2170.52 4915.75 3693.18 6545.25 7271.72 7741.63 11272.66 8234.6 21625.05 8912.48 5612.76 +V98 0 149.15 135.65 144.37 124.09 117.76 110.31 127.3 113.58 47.7 128.4 127.61 126.27 136.02 105.67 160.41 130.73 17.73 118.88 107.55 121.9 120.41 133.07 129.53 119.35 0 106.34 43.64 +V99 314.71 233.89 257.32 290.71 136.54 131.91 212.71 151.12 216.11 70.67 144.84 161.98 199.1 177.26 109.83 276.15 178.19 56.71 136.06 92.56 133.57 240.27 196.46 181.17 175.41 0 144.44 73.62 +V100 1063.57 888.31 802.4 899.21 524.53 465.73 990.79 508.3 767.86 235.42 425.38 531.11 631.35 755.31 380.35 795.06 586.43 170.6 399.27 323.3 426.24 771.87 698.1 557.47 570.57 1826.56 696.67 480.86 +V101 2587.9 1673.54 1654.1 1984.41 1404.72 1474.72 2767.56 1490.35 1879.66 525.82 725.28 1591.13 1128.98 1962.5 1210.7 1571.45 1365.01 433.48 897.88 885.71 1024.88 1264.44 2472.8 1515.25 1349.88 4852 1782.85 1340.9 +V102 3565.72 1975.42 2013.22 2140.6 1668.46 2455.07 3602.33 2361.46 2472.79 726.93 769.9 2420.79 1099.54 1908.1 1814.65 1765.41 1629.73 596.03 990.98 1185.95 1435.53 1123.37 4179.54 2564.22 1660.72 6490.51 2453.85 1944.54 +V103 0 48.29 0 0 0 0 70.19 0 14.81 28.04 0 0 0 0 0 0 0 0 0 123.9 0 0 0 0 0 5.93 16.23 43.56 +V104 0 123.49 65.51 80.81 98.52 68.99 195.36 83.25 89.49 55.5 97.05 128.29 99.81 113.05 120.62 0 93.14 47.16 119.68 367.75 78.17 59.42 81.7 79.25 121.63 0 113.45 109.53 +V105 0 85.23 0 0 0 0 168.05 0 31.66 62.66 0 0 0 0 0 0 0 0 0 233.87 0 0 0 0 0 0 29.23 82.69 +V106 0 183.94 76.89 113 125.6 0 370.73 0 108.77 125.97 150.38 121.92 135.84 186.45 103.87 0 116.41 63.52 154.21 496.94 107.83 94.48 106.85 0 141.87 0 137.77 156.29 +V107 423.7 0 164.21 507.86 578.77 522.85 0 346.55 317.99 234.19 0 299.3 343.68 661.93 499.17 759.59 427.28 274.44 363.88 432.47 486.04 383.04 381.67 0 497.37 0 318.06 202.18 +V108 4.6 2.76 2.42 3.59 3.85 3.27 5.32 4.47 3.79 0.98 4.96 3.56 3.84 4.62 5.72 5.58 4.72 0.89 3.99 4.66 4.99 4.79 4.25 2.82 3.33 4.09 4.11 0.74 +V109 1.46 1.14 1.27 1.13 1.52 1.57 1.35 1.14 1.32 0.18 1.18 1.28 1.13 1.2 1.14 1.63 1.26 0.19 1.32 0.9 1.14 1.6 1.07 1.42 1.87 0.91 1.28 0.34 +V110 0.52 0.55 0 0.49 0 0 0 0.51 0.26 0.28 0.35 0.38 0.56 0.44 0 0.55 0.38 0.2 0.32 0.37 0.35 0.52 0 0.44 0.44 0.28 0.34 0.16 +V111 0.4 0 0 0.43 0.32 0 0 0.39 0.19 0.21 0.3 0.37 0 0.4 0 0.42 0.25 0.2 0 0.36 0.25 0.47 0 0.39 0.38 0 0.23 0.2 +V112 0.76 0.49 0.43 0.64 0.49 0.48 0.23 0.71 0.53 0.17 0.47 0.52 0.59 0.62 0.38 0.65 0.54 0.1 0.32 0.49 0.38 0.55 0.49 0.6 0.64 0.47 0.49 0.11 +V113 0.61 0.58 0.53 0.53 0.45 0.31 0.15 0.51 0.46 0.15 0.36 0.51 0.44 0.45 0.48 0.66 0.48 0.1 0.33 0.53 0.37 0.61 0.36 0.51 0.67 0.33 0.46 0.13 +V114 0 0 0 0 0.09 0 0 0.12 0.03 0.05 0 0.1 0 0 0 0 0.02 0.04 0 0 0.1 0 0.12 0.11 0 0 0.04 0.06 +V115 0 0 0 0 0 0 0 0.13 0.02 0.04 0 0.11 0 0 0 0 0.02 0.05 0 0 0 0 0.15 0.12 0 0 0.03 0.06 +V116 1.76 1.89 1.43 1.19 1.34 1.64 0 2.33 1.44 0.68 1.16 2.16 0 1.74 2.23 1.12 1.4 0.83 0 1.47 1.37 1.34 2.27 1.83 1.51 1.43 1.4 0.65 diff -r ad06aeed02c9 -r db1d80e89156 runit/exa2/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/exa2/sampleMetadata.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,29 @@ +sampleMetadata meta1 +S1 A +S2 A +S3 A +S4 A +S5 A +S6 A +S7 A +S8 A +S9 B +S10 B +S11 B +S12 B +S13 B +S14 B +S15 B +S16 C +S17 C +S18 C +S19 C +S20 C +S21 C +S22 C +S23 C +S24 C +S25 BC +S26 AB +S27 BC +S28 AC diff -r ad06aeed02c9 -r db1d80e89156 runit/exa2/variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/exa2/variableMetadata.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,117 @@ +variableMetadata meta2 +V1 ER +V2 GGG +V3 GGG +V4 GGG +V5 GGG +V6 CE +V7 CE +V8 CE +V9 TG +V10 TG +V11 TG +V12 TG +V13 TG +V14 AM +V15 AM +V16 AM +V17 AM +V18 AM +V19 AM +V20 AM +V21 AM +V22 AM +V23 AM +V24 AM +V25 AM +V26 AM +V27 AM +V28 AM +V29 AM +V30 AM +V31 AM +V32 ER +V33 ER +V34 ER +V35 ER +V36 ER +V37 CER +V38 CER +V39 CER +V40 CER +V41 CER +V42 CER +V43 CER +V44 CER +V45 CER +V46 CER +V47 PP +V48 PP +V49 PP +V50 PP +V51 PP +V52 PP +V53 PP +V54 PP +V55 PP +V56 PP +V57 PP +V58 PP +V59 PP +V60 PP +V61 PP +V62 PP +V63 PP +V64 CC +V65 CC +V66 CC +V67 CC +V68 CC +V69 CC +V70 CC +V71 CC +V72 CC +V73 CC +V74 CC +V75 CC +V76 CC +V77 CC +V78 CC +V79 CC +V80 CC +V81 CC +V82 CC +V83 CC +V84 CC +V85 SM +V86 SM +V87 SM +V88 SM +V89 SM +V90 SM +V91 SM +V92 SM +V93 SM +V94 SM +V95 SM +V96 PI +V97 PI +V98 PI +V99 PI +V100 PI +V101 PI +V102 PI +V103 PI +V104 PI +V105 PI +V106 PI +V107 NG +V108 NG +V109 NG +V110 SO +V111 SO +V112 SO +V113 SO +V114 SO +V115 SO +V116 SO diff -r ad06aeed02c9 -r db1d80e89156 runit/heatmap_runtests.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/heatmap_runtests.R Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,105 @@ +#!/usr/bin/env Rscript + +## Package +##-------- + +library(RUnit) + +## Constants +##---------- + +testOutDirC <- "output" +argVc <- commandArgs(trailingOnly = FALSE) +scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)]) + + +## Functions +##----------- + +## Reading tables (matrix or data frame) +readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) { + + file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\".")) + + switch(typeC, + matrix = return(t(as.matrix(read.table(file = fileC, + header = TRUE, + row.names = 1, + sep = "\t", + stringsAsFactors = FALSE)))), + dataframe = return(read.table(file = fileC, + header = TRUE, + row.names = 1, + sep = "\t", + stringsAsFactors = FALSE))) + +} + +## Call wrapper +wrapperCallF <- function(paramLs) { + + ## Set program path + wrapperPathC <- file.path(dirname(scriptPathC), "..", "heatmap_wrapper.R") + + ## Set arguments + argLs <- NULL + for (parC in names(paramLs)) + argLs <- c(argLs, parC, paramLs[[parC]]) + + ## Call + wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ") + + if(.Platform$OS.type == "windows") + wrapperCallC <- paste("Rscript", wrapperCallC) + + wrapperCodeN <- system(wrapperCallC) + + if (wrapperCodeN != 0) + stop("Error when running heatmap_wrapper.R.") + + ## Get output + outLs <- list() + if ("dataMatrix_out" %in% names(paramLs)) + outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix") + if ("sampleMetadata_out" %in% names(paramLs)) + outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe") + if ("variableMetadata_out" %in% names(paramLs)) + outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe") + if("information" %in% names(paramLs)) + outLs[["infVc"]] <- readLines(paramLs[["information"]]) + + return(outLs) +} + +## Setting default parameters +defaultArgF <- function(testInDirC) { + + defaultArgLs <- list() + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv"))) + defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv") + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv"))) + defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv") + if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv"))) + defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv") + + defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv") + defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv") + defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv") + defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf") + defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt") + + defaultArgLs + +} + +## Main +##----- + +## Create output folder +file.exists(testOutDirC) || dir.create(testOutDirC) + +## Run tests +test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$') +isValidTestSuite(test.suite) +test.results <- runTestSuite(test.suite) +print(test.results) diff -r ad06aeed02c9 -r db1d80e89156 runit/heatmap_tests.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/heatmap_tests.R Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,57 @@ +test_input_cut4 <- function() { + + testDirC <- "input" + argLs <- list(disC = "1-cor", + cutSamN = "4", + cutVarN = "3", + corMetC = "spearman", + aggMetC = "ward", + colC = "blueOrangeRed", + scaL = "TRUE", + cexN = "0.8") + + argLs <- c(defaultArgF(testDirC), argLs) + outLs <- wrapperCallF(argLs) + + checkEqualsNumeric(outLs[['samDF']][13, 'heat_clust'], 4) + +} + +test_exa1_cut3 <- function() { + + testDirC <- "exa1" + argLs <- list(disC = "1-cor", + cutSamN = "3", + cutVarN = "4", + corMetC = "spearman", + aggMetC = "ward", + colC = "blueOrangeRed", + scaL = "TRUE", + cexN = "1") + + argLs <- c(defaultArgF(testDirC), argLs) + outLs <- wrapperCallF(argLs) + + checkEqualsNumeric(outLs[['varDF']]['V24', 'heat_clust'], 4) + +} + +test_exa2_cut4 <- function() { + + testDirC <- "exa2" + argLs <- list(disC = "1-cor", + cutSamN = "1", + cutVarN = "1", + corMetC = "spearman", + aggMetC = "ward", + colC = "blueOrangeRed", + scaL = "TRUE", + cexN = "1") + + argLs <- c(defaultArgF(testDirC), argLs) + outLs <- wrapperCallF(argLs) + + checkEquals(outLs[['varDF']]['V31', 'meta2'], 'AM') + +} + diff -r ad06aeed02c9 -r db1d80e89156 runit/input/dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/input/dataMatrix.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,16 @@ +dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 +HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 +HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 32742 +HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 1580343 39315 +HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 994336 239030 +HMDB00822 483755 579287 1132413 157113 1577570 1469735 1085454 477909 814755 245417 610681 763706 2406336 827531 992508 569605 355321 150259 1334200 271010 +HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 1517319 841661 +HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 1992420 284775 +HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 1061418 622898 +HMDB00518 34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 867108 73831 +HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 7517724 1341900 +HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 9120781 44276 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 3359238 2540044 +HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 1824553 387811 +HMDB00512 53304 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 438839 85554 +HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 454489 616061 diff -r ad06aeed02c9 -r db1d80e89156 runit/input/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/input/sampleMetadata.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,21 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 41 23.03 M +HU_028 7 pos 41 23.92 F +HU_034 9 pos 52 23.37 M +HU_051 20 pos 24 23.23 F +HU_060 24 pos 55 28.72 F +HU_078 34 pos 46 25.18 M +HU_091 42 pos 61 26.12 M +HU_093 43 pos 53 21.71 M +HU_099 46 pos 23 21.3 M +HU_110 53 pos 50 20.9 F +HU_130 63 pos 33 26.06 M +HU_134 67 pos 48 22.89 M +HU_138 68 pos 42 21.88 M +HU_149 72 pos 35 19.49 F +HU_152 75 pos 26 17.58 F +HU_175 87 pos 35 21.26 F +HU_178 88 pos 60 32.87 F +HU_185 95 pos 42 21.09 F +HU_204 104 pos 31 29.06 M +HU_208 106 pos 27 18.61 F diff -r ad06aeed02c9 -r db1d80e89156 runit/input/variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/input/variableMetadata.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,16 @@ +variableMetadata name +HMDB03193 Testosterone_glucuronide +HMDB01101 p-Anisic_acid +HMDB10348 Dehydroepiandrosterone_3-glucuronide +HMDB59717 Glu-Val +HMDB00822 p-Hydroxymandelic_acid +HMDB13189 3-Indole_carboxylic_acid_glucuronide +HMDB00299 Xanthosine +HMDB00191 L-Aspartic_acid +HMDB00518 Chenodeoxycholic_acid +HMDB00715 Kynurenic_acid +HMDB01032 Dehydroepiandrosterone_sulfate +HMDB00208 Oxoglutaric_acid +HMDB04824 N2,N2-Dimethylguanosine +HMDB00512 N-Acetyl-L-phenylalanine +HMDB00251 Taurine diff -r ad06aeed02c9 -r db1d80e89156 runit/output/dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/dataMatrix.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,16 @@ +dataMatrix HU_051 HU_208 HU_178 HU_130 HU_175 HU_099 HU_152 HU_204 HU_017 HU_138 HU_034 HU_078 HU_060 HU_149 HU_028 HU_093 HU_134 HU_091 HU_110 HU_185 +HMDB13189 619181 841661 2092753 1608814 2893445 3526136 3132404 1517319 2644620 1941527 1661412 2755434 136278 113937 727587 837865 3446611 593863 2003278 1034666 +HMDB00251 622468 616061 80614 310918 403815 268331 335711 454489 368600 577184 94936 293988 180988 10985 616555 767894 1248919 352855 167246 63393 +HMDB01101 3158 32742 31250 608298 1464339 976436 1107705 72900 30689 72021 52217 229568 10789748 442510 6877586 3878773 1605075 4763576 831937 2724553 +HMDB00191 392284 622898 710519 639437 1945577 960658 1246459 1061418 560002 1409045 575790 785428 888498 2292023 771533 591569 1092885 645785 910201 773384 +HMDB00208 1172376 2540044 7037373 2477288 10335722 5593888 8960828 3359238 747080 4230072 595872 3143654 7172632 7621236 13420742 1433702 3346077 4059767 5402629 1574738 +HMDB59717 67604 239030 784738 808334 1563158 1378535 715190 994336 357351 871209 301983 1028110 306862 895435 1030464 270027 1132813 1530493 289677 146195 +HMDB00512 85009 85554 827723 569970 1171008 342532 542345 438839 53304 246282 280560 556003 1333877 1140422 319783 209285 525240 590779 198512 222953 +HMDB00518 NA 73831 514579 440223 28361 230242 48673 867108 34236 10657 85944 129886 342102 419508 58249 13154 315368 175800 NA 23108 +HMDB00822 157113 271010 355321 610681 569605 814755 992508 1334200 483755 2406336 1132413 1469735 1577570 827531 579287 477909 763706 1085454 245417 150259 +HMDB00715 371059 1341900 2295288 4184204 3577833 2558923 3820724 7517724 1252089 3236644 905408 5140022 4983588 2615560 2547452 814523 3865723 2658555 859466 625924 +HMDB01032 430453 44276 871010 31151730 5588731 59906109 20249262 9120781 2569205 14989438 1604999 26222916 8103558 1554658 26023086 675754 18648127 257139 263055 15920 +HMDB00299 159386 284775 411886 504108 566050 768004 1110050 1992420 250551 1362408 456162 808657 1013302 1057660 1046138 250403 1014041 614370 242085 142233 +HMDB04824 178517 387811 782673 477995 1020206 1253319 1411802 1824553 374028 1157093 539206 959381 1046190 1089284 1144386 310260 825691 605191 477259 346761 +HMDB03193 27242 43907 79673 339188 212500 559869 451270 891129 76043 262271 44943 173175 436566 127285 412165 57066 471368 242549 3732 NA +HMDB10348 34582 39315 214392 279156 161069 610110 433529 1580343 47259 451573 60885 168264 529874 591487 544877 76457 524468 176500 16262 13781 diff -r ad06aeed02c9 -r db1d80e89156 runit/output/essai.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/essai.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,21 @@ +sampleMetadata injectionOrder mode age bmi gender heat_clust +HU_017 2 pos 41 23.03 M 1 +HU_034 9 pos 52 23.37 M 1 +HU_204 104 pos 31 29.06 M 2 +HU_134 67 pos 48 22.89 M 2 +HU_099 46 pos 23 21.3 M 2 +HU_078 34 pos 46 25.18 M 2 +HU_130 63 pos 33 26.06 M 2 +HU_028 7 pos 41 23.92 F 2 +HU_138 68 pos 42 21.88 M 2 +HU_152 75 pos 26 17.58 F 2 +HU_051 20 pos 24 23.23 F 3 +HU_208 106 pos 27 18.61 F 3 +HU_110 53 pos 50 20.9 F 3 +HU_178 88 pos 60 32.87 F 3 +HU_149 72 pos 35 19.49 F 3 +HU_175 87 pos 35 21.26 F 3 +HU_060 24 pos 55 28.72 F 4 +HU_091 42 pos 61 26.12 M 4 +HU_093 43 pos 53 21.71 M 4 +HU_185 95 pos 42 21.09 F 4 diff -r ad06aeed02c9 -r db1d80e89156 runit/output/figure.pdf Binary file runit/output/figure.pdf has changed diff -r ad06aeed02c9 -r db1d80e89156 runit/output/information.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/information.txt Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,24 @@ + +Start of the 'Heatmap' module: Tue 02 Aug 2016 11:48:22 AM + +Arguments used: + + value +dataMatrix_in "tests/input/dataMatrix.tsv" +sampleMetadata_in "tests/input/sampleMetadata.tsv" +variableMetadata_in "tests/input/variableMetadata.tsv" +dataMatrix_out "tests/output/dataMatrix.tsv" +sampleMetadata_out "tests/output/sampleMetadata.tsv" +variableMetadata_out "tests/output/variableMetadata.tsv" +figure "tests/output/figure.pdf" +information "tests/output/information.txt" +disC "1-cor" +cutSamN "4" +cutVarN "3" +corMetC "spearman" +aggMetC "ward" +colC "blueOrangeRed" +scaL "TRUE" +cexN "0.8" + +End of the 'Heatmap' Galaxy module call: Tue 02 Aug 2016 11:48:22 AM diff -r ad06aeed02c9 -r db1d80e89156 runit/output/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/sampleMetadata.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,21 @@ +sampleMetadata injectionOrder mode age bmi gender heat_clust +HU_051 20 pos 24 23.23 F 3 +HU_208 106 pos 27 18.61 F 3 +HU_178 88 pos 60 32.87 F 1 +HU_130 63 pos 33 26.06 M 1 +HU_175 87 pos 35 21.26 F 1 +HU_099 46 pos 23 21.3 M 1 +HU_152 75 pos 26 17.58 F 1 +HU_204 104 pos 31 29.06 M 1 +HU_017 2 pos 41 23.03 M 1 +HU_138 68 pos 42 21.88 M 1 +HU_034 9 pos 52 23.37 M 1 +HU_078 34 pos 46 25.18 M 1 +HU_060 24 pos 55 28.72 F 4 +HU_149 72 pos 35 19.49 F 4 +HU_028 7 pos 41 23.92 F 2 +HU_093 43 pos 53 21.71 M 2 +HU_134 67 pos 48 22.89 M 2 +HU_091 42 pos 61 26.12 M 2 +HU_110 53 pos 50 20.9 F 2 +HU_185 95 pos 42 21.09 F 2 diff -r ad06aeed02c9 -r db1d80e89156 runit/output/variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runit/output/variableMetadata.tsv Sat Aug 06 12:18:15 2016 -0400 @@ -0,0 +1,16 @@ +variableMetadata name heat_clust +HMDB13189 3-Indole_carboxylic_acid_glucuronide 3 +HMDB00251 Taurine 3 +HMDB01101 p-Anisic_acid 2 +HMDB00191 L-Aspartic_acid 2 +HMDB00208 Oxoglutaric_acid 2 +HMDB59717 Glu-Val 2 +HMDB00512 N-Acetyl-L-phenylalanine 2 +HMDB00518 Chenodeoxycholic_acid 1 +HMDB00822 p-Hydroxymandelic_acid 1 +HMDB00715 Kynurenic_acid 1 +HMDB01032 Dehydroepiandrosterone_sulfate 1 +HMDB00299 Xanthosine 1 +HMDB04824 N2,N2-Dimethylguanosine 1 +HMDB03193 Testosterone_glucuronide 1 +HMDB10348 Dehydroepiandrosterone_3-glucuronide 1 diff -r ad06aeed02c9 -r db1d80e89156 tests/exa1/dataMatrix.tsv --- a/tests/exa1/dataMatrix.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -dataMatrix S1 S2 S3 S4 S5 S6 -V1 196502 237810 198284 182894 105331 132150 -V2 2544571 2614302 2451909 3142179 3768416 3713752 -V3 1230784 1161975 1143745 1150915 1344578 1220503 -V4 1630089 1818363 1563465 2387030 3502620 2954208 -V5 2184963 2374515 1974647 2313226 1782744 1860757 -V6 5262172 6365930 5010369 9109487 6410977 6378638 -V7 2232587 2745906 2200995 3832216 2708070 2869295 -V8 483320 660332 433486 1062013 677822 748514 -V9 112905 136174 123604 162138 240686 195271 -V10 179154 195001 180519 98623 132470 123032 -V11 175220 169515 158401 111215 103539 159727 -V12 46503 55313 76310 46932 92318 43629 -V13 113796 91557 95960 92685 140973 112898 -V14 540798 596737 511783 876548 1626199 1385367 -V15 140806 135469 145016 229518 434119 398941 -V16 1334798 1318651 1308783 2345055 4068874 3565724 -V17 1083792 1145232 916864 838363 1678307 1304234 -V18 91671 101007 79999 85402 146939 126314 -V19 274181 282331 292645 394175 330817 293481 -V20 879658 809068 903330 1273966 959314 938277 -V21 608434 662366 727426 920178 1106194 1201520 -V22 1600960 1545158 1608816 1880288 2246189 2069613 -V23 2171614 2239769 2106004 2565354 4913676 4072322 -V24 4045143 3862213 4053630 7352540 5574415 6185035 -V25 202805 182042 165499 57267 86611 89320 -V26 586997 667911 522193 748212 595063 659353 -V27 229790 256287 253497 1189248 1025521 746948 -V28 1644853 1759382 1760494 3379214 4572430 4386799 -V29 8491372 9275641 8655578 12105700 13265172 13484917 -V30 724039 730730 640992 1475658 1191085 1213210 -V31 86524840 89500400 88593487 183705591 150949959 169189091 -V32 26916143 30167854 28256416 39049936 45546213 47237473 -V33 2683733 2654918 2386486 4786536 3622659 3879731 -V34 3919797 4529379 3595989 7965534 5963667 6339219 -V35 84384696 90691983 83322980 51888441 86013709 79735533 -V36 95751916 101056674 92760886 129551865 109580811 118980909 -V37 374328 416298 355931 255675 371223 338701 -V38 2219529 2333885 2206832 903780 981633 1136522 diff -r ad06aeed02c9 -r db1d80e89156 tests/exa1/sampleMetadata.tsv --- a/tests/exa1/sampleMetadata.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -sampleMetadata smeta1 smeta2 -S1 196502 2544571 -S2 237810 2614302 -S3 198284 2451909 -S4 182894 3142179 -S5 105331 3768416 -S6 132150 3713752 diff -r ad06aeed02c9 -r db1d80e89156 tests/exa1/variableMetadata.tsv --- a/tests/exa1/variableMetadata.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -variableMetadata vmeta1 vmeta2 vmeta3 vmeta4 vmeta5 vmeta6 -V1 196502 237810 198284 182894 105331 132150 -V2 2544571 2614302 2451909 3142179 3768416 3713752 -V3 1230784 1161975 1143745 1150915 1344578 1220503 -V4 1630089 1818363 1563465 2387030 3502620 2954208 -V5 2184963 2374515 1974647 2313226 1782744 1860757 -V6 5262172 6365930 5010369 9109487 6410977 6378638 -V7 2232587 2745906 2200995 3832216 2708070 2869295 -V8 483320 660332 433486 1062013 677822 748514 -V9 112905 136174 123604 162138 240686 195271 -V10 179154 195001 180519 98623 132470 123032 -V11 175220 169515 158401 111215 103539 159727 -V12 46503 55313 76310 46932 92318 43629 -V13 113796 91557 95960 92685 140973 112898 -V14 540798 596737 511783 876548 1626199 1385367 -V15 140806 135469 145016 229518 434119 398941 -V16 1334798 1318651 1308783 2345055 4068874 3565724 -V17 1083792 1145232 916864 838363 1678307 1304234 -V18 91671 101007 79999 85402 146939 126314 -V19 274181 282331 292645 394175 330817 293481 -V20 879658 809068 903330 1273966 959314 938277 -V21 608434 662366 727426 920178 1106194 1201520 -V22 1600960 1545158 1608816 1880288 2246189 2069613 -V23 2171614 2239769 2106004 2565354 4913676 4072322 -V24 4045143 3862213 4053630 7352540 5574415 6185035 -V25 202805 182042 165499 57267 86611 89320 -V26 586997 667911 522193 748212 595063 659353 -V27 229790 256287 253497 1189248 1025521 746948 -V28 1644853 1759382 1760494 3379214 4572430 4386799 -V29 8491372 9275641 8655578 12105700 13265172 13484917 -V30 724039 730730 640992 1475658 1191085 1213210 -V31 86524840 89500400 88593487 183705591 150949959 169189091 -V32 26916143 30167854 28256416 39049936 45546213 47237473 -V33 2683733 2654918 2386486 4786536 3622659 3879731 -V34 3919797 4529379 3595989 7965534 5963667 6339219 -V35 84384696 90691983 83322980 51888441 86013709 79735533 -V36 95751916 101056674 92760886 129551865 109580811 118980909 -V37 374328 416298 355931 255675 371223 338701 -V38 2219529 2333885 2206832 903780 981633 1136522 diff -r ad06aeed02c9 -r db1d80e89156 tests/exa2/dataMatrix.tsv --- a/tests/exa2/dataMatrix.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,117 +0,0 @@ -dataMatrix S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15 S16 S17 S18 S19 S20 S21 S22 S23 S24 S25 S26 S27 S28 -V1 1484.78 1106.3 1217.84 1441.38 1213.63 1302.49 1412.79 1322.28 1258.89 1365.49 1146.78 1243 1242.47 1250.61 1307.52 1423.59 1290.51 1126.64 1421.23 1235.75 1084.56 1252.87 1254.74 1584.64 1474.43 1283.85 1347.74 1557.35 -V2 0 0 0 13.14 0 0 0 16.36 0 0 11.8 0 0 0 0 12.34 12.45 0 0 6.87 6.41 0 15.53 12.87 0 14.58 0 0 -V3 0 5.93 7.82 16.41 7.58 9.54 8.25 20.52 5.89 6.27 20.86 5.2 8.97 10.93 6.51 21.06 25.05 0 0 11.79 16.97 7.23 19.58 20.56 11.07 20.87 0 6.18 -V4 10.86 12.56 7.93 14.32 10.64 11.38 8.24 15.8 11.75 11.29 12 6.34 8.05 16.12 13.33 18.81 24.44 8.26 6.99 9.76 10.29 9.11 19.32 26.55 15.58 17.38 3.31 7.2 -V5 9.49 5.72 6.96 5.48 6.38 9.57 6.31 8.67 8.21 9.1 9.23 9.68 7.1 6.89 4.39 7.98 11.58 7.71 10.99 8.67 13.18 7.19 10.96 5.86 7.98 10.39 4.69 11.78 -V6 43.5 19.95 34.96 31.98 31.27 49.9 38.17 26.44 27.19 40.64 40.9 47 26.26 30.31 20.64 49.54 49.06 26.73 64.56 43.29 80.61 38.08 42.01 37.22 26.37 25.97 25.2 41.05 -V7 333.79 311.77 321.24 391.51 297.03 263.85 246.39 221.76 447.49 418.79 300.37 414.43 262.68 244.09 213.24 423.97 523.16 344.76 413.98 402.45 251.38 225.47 300.48 230.58 301.51 246.9 361.04 375.51 -V8 49.48 20.81 27.33 17.44 15.39 14.84 17.67 13.41 29.27 63.13 34.04 23.41 25.16 16.2 11.68 42.53 31.46 12.83 38.02 40.28 25.77 12.44 41.05 15.25 23.21 27.11 25.98 22.33 -V9 2.56 1.18 1.07 1.39 2.59 2.53 1.98 3.84 1.61 1.72 1.76 1.73 0.63 2.13 2.02 2.44 0 1.24 1.22 1.87 7.83 4.15 5.88 4.77 5.77 7.81 0 1.67 -V10 6.37 4.55 2.63 5.09 6.29 6.32 6.31 6.61 4.35 5.98 4.79 6.3 1.24 6.98 5.09 6.64 7.21 3.63 4.14 5.47 19.45 8.4 9.41 10.83 10.78 11.98 1.29 3.86 -V11 11.9 21.21 10.67 19.08 17.84 10.64 13.61 10.41 17.75 17.87 13.24 15.27 7.83 18.66 13.5 18.67 26.37 14.46 13.18 18.29 26.21 10.65 16.46 21.52 19.57 17.89 8.81 10.4 -V12 4.38 8.56 4.95 8.83 5.87 3.53 5.15 0.45 7.67 5.85 5.32 4.88 4.55 5.87 5.12 6.16 10.97 6.67 4.69 6.11 7.33 3.34 5.44 8.94 5.83 5.07 5.77 3.8 -V13 0.78 1.17 0.61 1.21 0.89 0 0.56 0.45 1.04 1.03 0 0.71 0.62 0.78 0 1.25 0 0.63 1.1 1.16 1.13 0 0.87 1.05 1.06 0.63 0.36 0.82 -V14 1511.11 1158.59 1529.32 1471.39 1654.17 2320.94 2630.11 2148.49 1248.21 1590.03 1120.83 1388.4 1523.12 2293.02 0 1566.36 1543.42 842.31 1421.66 1850.9 2870.84 2338.83 1979.28 3581.78 1757.49 2983.66 2967.62 1392.97 -V15 638.35 560.78 803.6 597.71 719.25 805.09 773.49 777.4 566.6 780.02 607.71 493.24 655.73 880.88 0 768.64 625.98 451.52 443.79 745.64 692.9 839.58 727.49 1376.26 622.72 1421.07 997.77 827.06 -V16 165.37 51.55 130.59 57.95 98.46 310.56 233.32 147.43 39.69 109.04 0 101.57 0 97.94 0 107.15 90.92 0 177.32 137.54 432.77 267.66 128.29 331.03 144.05 118.52 162.61 64.33 -V17 1586.23 2103.69 1926.52 1614.01 2166.04 2284.19 2506.01 2040.02 1327.06 1705.97 1461.31 1649.21 1759.17 2442.95 0 1875.52 1881.42 1512.88 1520.67 1981.82 3021.6 2389.78 2088.67 4697.26 1646.11 3269.32 2805.59 2315.4 -V18 243.32 227.33 349.71 195.5 327.78 307.89 703.12 197.9 0 234.07 330.09 246.26 256.2 419.19 0 265.17 192.4 188.52 255.13 481.91 462.41 216.66 336.29 478.85 152.09 424.2 257.62 198.53 -V19 1921.6 2015.61 2872.21 2975.67 2406.07 2438.08 2381.42 2789.98 2881.8 2119.69 1953.23 1880.63 1985.58 1819.19 0 2343.84 2473.67 1909.11 1798.62 2824.34 1735 2429.73 1958.41 4299.39 2609.31 3374.62 2824.95 3079.01 -V20 539.06 432.85 724.98 347.76 380.87 522.5 444.07 550.04 502.86 576.95 744.34 410.58 415.64 321.36 0 805.68 451.18 292.67 471.68 793.63 804.05 679.41 0 1047.85 444.04 444.5 547.87 738.82 -V21 288.7 0 0 0 0 0 0 0 0 144.5 0 0 0 154.85 0 119.48 0 0 0 0 0 0 0 179.2 0 208.44 0 0 -V22 273.95 149.66 287.92 0 327.34 0 717.56 0 0 311.8 0 121.95 0 172.76 0 238.66 161.38 0 0 0 0 0 608.86 398.84 173.3 462.34 347.64 312.02 -V23 614.701 98.849 0 217.085 320.044 246.769 107.187 114.252 185.453 0 0 179.589 0 0 0 169.996 58.781 133.231 209.81 106.94 159.654 97.758 160.071 0 131.035 0 169.996 0 -V24 7.329 7.035 6.437 5.973 6.656 0 0 6.663 7.697 7.511 6.876 7.531 6.817 6.579 5.978 0 7.191 7.57 6.105 6.994 6.84 0 0 0 7.322 7.182 0 5.935 -V25 28.846 26.604 26.246 0 25.943 0 24.929 0 29.452 27.652 28.324 28.299 0 0 24.957 0 28.278 28.029 25.955 27.292 27.437 24.795 0 0 0 26.468 0 0 -V26 16.71 15.574 15.343 0 0 14.629 0 16.021 18.624 16.703 16.82 15.859 15.086 14.725 14.543 0 16.698 16.782 14.461 16.186 16.36 0 0 14.682 0 14.853 0 14.503 -V27 187.78 134.86 104.51 164.53 145.23 101.57 194.53 143.99 147.12 34.35 110 105.84 95.85 160.24 97.8 108.21 112.99 23.83 110.36 146.6 127.22 132.54 134.6 123.13 156.39 138.56 133.67 14.17 -V28 20.22 14.96 11.79 17.94 16.79 11.55 22.08 17.8 16.64 3.74 13.56 12.82 11.43 19.05 11.62 12.97 13.58 2.8 13.44 17.3 15.87 14.87 16.1 14.06 16.01 17.45 15.64 1.43 -V29 75.78 77.98 38.21 69.93 86.6 35.94 93.92 70.68 68.63 21.05 45.99 55.4 45.65 58.75 39.82 34.02 46.6 9.28 29.73 65.55 65.73 62.13 56.75 35.83 61.46 60.77 54.74 13.94 -V30 12.75 14.38 8.06 13.79 15.45 7.33 16.09 14.9 12.84 3.34 8.78 11.42 9.47 12.32 7.87 7.82 9.61 1.87 8.15 11.43 13.59 8.63 11.36 8.74 10.62 15.01 10.94 2.45 -V31 152.24 143.82 99.08 127.98 140.79 77.54 137.85 112.09 123.92 25.64 107.74 112.76 89.79 107.46 71.99 82.81 95.43 16.35 78.04 79.82 132.59 126.74 133.86 82.86 109.23 124.44 108.45 24.55 -V32 938.99 725.51 504.85 599.76 701.02 393.83 668.81 533.32 633.26 165.95 562.51 557.52 415.33 598.74 338.85 352.62 470.93 115.55 385.39 327.2 589.46 648.36 743.1 360.36 591.98 574.85 527.59 150.99 -V33 2988.64 2781 2451.36 2290.88 2497.75 1772.76 2434.42 2222.88 2429.96 365.39 2071.07 2358.74 1919.88 2141.82 1236.79 1292.48 1836.8 465.52 1668.16 1167.73 2095.17 3286.45 2900.66 1323.11 2346.08 2245.29 2129.08 735.12 -V34 1644.27 1378.93 970.38 1310.7 1277.11 838.94 1276.17 1038.97 1216.93 256.38 1070.93 1248.62 908.78 1301.31 795.45 690.35 1002.58 246.43 1039.85 738.11 1609.77 1444.48 1417.84 843.04 1359.28 1512.42 1245.6 326.87 -V35 34.28 28.91 29.9 31.11 38.88 17.48 39.24 23.23 30.38 7.43 19.24 32.68 22.86 29.83 13.98 13.69 22.05 7.96 21.14 30.86 25.14 34.58 29.31 14.04 32.27 29.3 27.08 6.72 -V36 34.69 25.94 25.12 31.06 34.84 18.45 27.52 20.78 27.3 6.01 16.27 32.31 21.57 24.55 15.88 13.34 20.65 7.03 16.83 25.77 27.02 38.17 26.83 15.03 36.42 32.65 27.34 8.39 -V37 53.33 33.39 38.28 56 18.46 33.81 39.24 25.03 37.19 12.79 19.02 29.64 29.32 36.33 21.06 26.69 27.01 6.3 24.3 49.3 23.38 133.19 49.05 20.55 57.23 32.46 48.68 36.85 -V38 55.46 32.06 38.14 73.93 17.66 27.63 40.29 24.64 38.73 18.25 17.06 30.63 28.54 39.35 15.18 27.94 26.45 9.01 22.52 62.43 17.96 222 42.3 16.94 65.81 35.65 60.7 67.84 -V39 1615.79 832.94 948.85 1163.14 780.73 932.8 827.92 651.39 969.19 300.59 651.84 688.09 704.96 886.23 511.33 657.76 683.37 120.74 872.17 1307.25 802.54 2032.41 1544.2 758.36 1356.28 1432.05 1263.16 435.85 -V40 1699.27 766.05 997.32 1114.23 990.02 987.62 890.66 680.92 1015.76 309.1 716.86 590.9 623.14 866.72 485.55 674.31 659.58 128.63 766 948.5 764.57 1414.08 1579.67 769.54 1269.34 1677.86 1148.7 383.33 -V41 3995.34 1888.42 2393.66 1835.16 1684.97 1796.85 1192.55 1091.08 1984.75 909.69 1763.01 1285.69 1150.88 1126.86 1048.41 1193.59 1261.41 257.87 1437.84 1248.8 1395.5 2019.26 3393.17 1548.47 2189.84 2792.08 2003.12 761.04 -V42 6200.76 2703.73 3569.72 2967.38 2647.22 2701.52 1896.29 1731.65 3052.28 1397.8 2729.69 1770.64 1689.06 1813.5 1552.25 1977.75 1922.15 419.79 2262.29 1830.99 2226.75 2961.28 5042.17 2440.05 3329.37 4602.08 3086.87 1171.63 -V43 2766.76 1286.7 1535.67 1776.16 1043.65 1253.94 1165.85 989.89 1477.33 581.17 1081.96 962.62 1015.15 1217.68 877.56 1123.53 1046.42 120.87 1150.86 1405.41 1211.44 2590.33 1996.95 1466.31 2124.7 2561.89 1813.49 583.43 -V44 1808.56 1052.58 1064.38 1465.2 861.99 1062.52 1290.66 962.53 1196.05 311.32 811.08 1038.58 980.55 1253.84 820.41 794.37 949.8 179.67 766.54 1582.99 1107.43 3061.94 1384.89 1171.4 1849.11 2223.83 1643.52 731.04 -V45 361.49 289.55 263.82 424.39 250.66 201.69 240.88 240.95 284.18 73.44 248.27 273.46 216.48 217.64 165.11 174.49 215.91 41.61 227.97 327.36 274.12 615.76 379.63 251.66 345.47 506.13 366.01 133.46 -V46 2607.82 2000.16 1671.95 2357.94 1683.26 1571.32 1935.52 1840.49 1958.56 359.59 1995.27 1867.04 1691.03 1610.68 1121.25 1356.18 1606.91 323.82 1288.12 2384.86 1957.6 4620.77 2142.9 2097.88 2778.2 3638.56 2613.61 1057.86 -V47 4306.74 3278.54 2766.81 3676.12 2584.89 2707.8 3218.81 3013.78 3194.19 573.31 3189.42 3307.49 2902.72 2845.79 2162.9 2270.99 2779.88 470.14 2005.07 3846.66 3287.96 7678.68 3441.2 3648.6 4534.31 6234.27 4334.59 1807.15 -V48 2757.36 1972.09 1921.97 2047.43 2307.53 3450.36 2481.9 3192.32 2516.37 573.41 1605.23 4187.86 1340.3 2548.83 2241.75 1147.41 2178.56 1120.09 946.32 1988.3 3012.52 4348.05 4947.77 2894.49 2605.46 6227.79 3371.34 1704.39 -V49 2846.27 2112.17 2074.85 2484.04 2030.38 2892.38 2323.34 2689.36 2431.6 349.58 1659.98 3637.59 1615.48 2586.62 2360.5 1413.49 2212.28 835.81 1208.92 2272.05 2841.18 5130.58 4188 2879.36 2853.44 5754.18 3390.96 1517.17 -V50 63.24 68.39 44.94 64.93 37.36 31.18 60.74 35.49 50.78 15.1 52.13 43.34 53.45 55.07 31.66 31.25 44.48 10.88 33.05 60.72 34.37 209.37 55.71 37.41 51.12 69.22 68.87 58.26 -V51 1745.37 1185.09 1129.87 1082.42 1354.59 1492.4 1089.89 1391.1 1308.84 232.89 1028.07 1955.9 729.97 1004.49 961.76 574.74 1042.49 481.45 420.8 926.39 1134.46 2690.76 2585.95 984.56 1268.87 2558.63 1571.3 896.32 -V52 2325.89 1572.13 1488.2 1298.49 1823.74 2252.49 1456.85 2073.13 1786.37 391.59 1356.24 2938.31 868.29 1287.9 1431.16 730.25 1435.36 788.12 531.96 1115.79 1682.73 2924.65 3710.59 1520.02 1620.38 3734.6 2105.09 1202.01 -V53 352.51 261.05 248.74 309.45 289.73 416.53 266.85 428.71 321.69 70.28 236.94 537.25 193.5 326 319.28 189.21 300.36 130.33 152.84 203.76 442.22 511.73 516.04 437.43 331.36 880.17 434.44 225.04 -V54 216.14 119.32 400.57 336.36 56.47 89.37 155.36 49.48 177.88 130.48 97.22 114.95 135.48 117.64 76.58 160.44 117.05 29.18 83.99 83.8 18.56 195.87 181.22 21.21 196.54 152.66 116.73 74.64 -V55 3354.74 1889.02 3463.96 2595.51 1095.04 1188.43 1840.09 983.93 2051.34 989.95 1188.04 1824.94 1599.03 1844.36 1384.25 1654.65 1582.54 256.02 1244.41 1674.07 559.55 2535.71 2199.75 710.19 2034.19 3209.59 1770.93 909.24 -V56 689.37 323.77 632.5 615.72 142.49 199.66 291.67 166.84 382.75 226.87 180.91 296.75 246.47 305.63 207.47 338.53 262.63 61.25 203.85 288.31 71.53 584.03 353.14 107.89 389.42 519.26 314.68 183.74 -V57 6414.27 4067.65 4605.44 4227.56 3397.35 4016.57 3910.51 3544.13 4272.94 943.77 3394.68 4289.36 3906.95 4409.8 3951.68 4184.76 4022.87 363.34 3950.15 6095.62 3268.86 5116.94 4149.28 5007.15 4429.98 9674.53 5211.56 1994.81 -V58 6266.36 3952.06 4638.28 5920.74 2062.48 2497.54 4169.02 3215.66 4090.27 1503.58 1974.3 2964.15 3022.96 3735.08 2495.87 3708.52 2983.48 685.38 2577.02 5480.39 1887.75 9838.32 2801.7 2511.25 3945.65 6713.94 4469.5 2726.1 -V59 2080.03 874.53 1695.81 1374.04 1394.91 765.07 1135.71 1004.63 1290.59 440.83 1819.62 1091.7 968.82 881.98 936.64 1111.28 1135.01 347.02 942.22 791.46 436.14 1258.84 1124.31 632.85 885.87 2287.78 1044.93 565.34 -V60 4019.07 2882.43 2920.72 2773.03 2331.94 2583.34 2238.8 2947.54 2837.11 547.71 2278.86 2457.49 2253.88 2589.84 2426.05 2732.92 2456.51 183.15 2860.57 3738.87 2620.94 4076.27 2372.31 3116.74 2923.46 6850.52 3569.96 1439.67 -V61 30316.42 25360.24 24223.65 23154.87 18133.87 22307.77 23062.85 23590.21 23768.74 3389.17 15197.09 21838.91 19822.74 25644.43 20471.11 22104.93 20846.53 3426.18 25946.74 31472.14 23168.38 33432.4 20220.09 23962.44 22402.54 56752.04 29669.59 11842.22 -V62 62402.87 35366.22 42321.8 31258.28 45712.77 37769.84 37522.2 43278.66 41954.08 9480.21 43459.12 35791.78 33007.49 37555.87 30867.86 39466.54 36691.44 4528.68 42271.25 38040.41 33835.98 31348.66 36815.48 42979.08 35687.18 100505.6 45185.45 22694.47 -V63 5345.95 2464.9 3091.4 2805.39 3415.52 2539.93 3108.55 3202.34 3246.75 909.16 3585.55 2965.11 2611.3 2390.26 2831.05 3065.67 2908.16 412.12 2899.18 2910.75 2276.04 2502.17 3031.16 2991.49 2581.47 8752.35 3493.07 2141.79 -V64 5292.96 4008.72 4012.44 3886.04 3647.09 4488.47 3153.78 4115.83 4075.66 624.71 3329.53 3032.83 2312.02 3514.26 3087.36 3808.11 3180.69 512.3 5079.61 5010.13 3983.6 3431.06 4013.46 4214.52 3237.19 10957.47 4990.88 2498.27 -V65 25444.34 13558.49 16493.22 12642.32 18907.52 18009.06 14231.51 18620.1 17238.32 4086.37 19094.31 14715.79 12230.13 14978.12 11587.05 17803.28 15068.11 2966.33 20658.33 15965.36 15559.69 10040.91 15401.79 19709.15 13056.25 46168.25 19569.97 11265.33 -V66 13899.53 8944.63 10159.96 11074.5 10592.6 8214.08 10176.94 9842.82 10363.13 1692.08 10224.02 8347.23 9132.47 9222.4 7107.34 10746.74 9130.03 1305.62 12811.74 12563.23 8865.71 12920.36 8100.75 11165.92 10182.24 27260.68 12983.83 6047.39 -V67 23512.63 13724.09 15652.33 13277.44 14818.7 9962.66 15178.26 16531.8 15332.24 3861.68 16746.25 14037.72 17098.1 13131.82 11032.59 15239.5 14547.66 2299.46 12753.96 18982.74 12462.65 21193.96 9974.96 15787.58 16677.68 36925.01 18094.82 8438.68 -V68 821.85 585.07 674.53 840.2 718.19 574.86 651.98 653.13 689.98 98.6 706.95 560.39 503.06 591.94 388.25 697.71 574.72 120.85 1200.77 898.01 617.64 580.33 598.67 661.06 518.03 1915.59 873.76 476.91 -V69 5665.21 3978.35 4089.75 6323.17 5026.21 3349.48 4344.41 4708.65 4685.65 964.71 5080.09 3035.72 3840.01 3568.7 2368.7 4560.78 3742.33 988.46 7508.69 6081.63 3875.94 4956.96 3618.8 4029.91 4201.27 11407.44 5710.08 2652.15 -V70 22886.12 12566.47 13528.14 14763.84 14470.03 10368.79 13211.34 16198.81 14749.19 3707.08 18464.21 12968.59 14976.46 11752.16 9218.14 15570.81 13825.06 3229.53 15895.44 17072.56 12786.98 16896.42 8923.53 16188.56 14585.89 34726.7 17134.51 7604.44 -V71 11423.67 7260.23 8970.27 7850.77 7000.97 7015.29 6913.61 7283.92 7964.84 1553.03 6763.98 8126.89 6577.43 7492.23 8528.18 8010.27 7583.16 782.55 8054.41 8188.51 6660.61 8871.33 7225.66 8376.3 7110.27 20520.68 9375.97 4562.98 -V72 15637.27 10686.69 12884.29 7658.22 11941.71 16143.55 12067.08 13664.64 12585.43 2720.13 8240.99 12552.56 6342.23 11346.03 11072.08 8526.86 9680.13 2345.48 10280.75 9082.97 11453.12 8256.47 14972.26 12789.22 8817.57 34220.75 13734.14 8577.94 -V73 135.27 87.47 100.36 112.7 84.8 79.57 89.6 87.62 97.17 18.55 90.81 70.86 83.71 83.59 71.35 94.23 82.42 9.69 140.04 119.03 80.9 117.49 74.17 97.09 93.08 275.42 124.65 64.66 -V74 14754.19 9880.17 10295.05 8265.04 9657.1 14237.48 10965.97 14015.39 11508.8 2467.86 7500.76 12549.98 5789.86 8750.01 8146.62 7193.56 8321.8 2299.97 8467.08 8028.29 8820.04 6808.25 13820.28 11066.16 7654.05 27388.57 11506.59 6795.54 -V75 5044.67 4123.9 3380.68 3943.65 4810.8 3194.4 5781.71 4796.76 4384.57 880.42 3954.38 4991.5 3876.63 4266.2 4298.95 3072.12 4076.63 630.29 4034.2 4324.63 2909.16 3440.2 4620.79 2600.36 4008.27 5293.72 3903.92 890.76 -V76 27989.88 27031.11 27818.36 26202.32 31496.87 31500.9 29211.25 33237.97 29311.08 2502.57 30111.45 28276.59 27232.92 31880.59 26296.06 28183.17 28663.46 2023.76 31918.73 34538.92 29086.99 27914.54 27498.1 39484.04 33320.98 43351.62 33389.24 5645.12 -V77 6033.59 5638.84 5757.39 5676.17 6856.34 6971.39 5687.13 8714.58 6416.93 1072.27 6824.08 6173.48 5757.01 6766.91 5862.96 6737.69 6353.69 483.48 7038.06 7289.71 6550.93 6474.58 6456.35 8406.92 5959.81 9192.51 7171.11 1101.49 -V78 7531.71 9766.33 7917.05 7066.02 12533.47 8597.12 10418.97 11146.66 9372.17 1920.47 9102.5 9784.31 7945.3 9496.2 8096.37 6447.88 8478.76 1239.67 6847.86 10800.66 8877.01 9466.25 7931.75 8909.79 9603.09 8932.52 8921.12 1169.52 -V79 3370.7 4671.45 3614.71 3446.79 5356.27 4618.38 4037.77 7068.76 4523.1 1239.4 4406.1 4263.32 3463.28 4600.41 3959.76 3752.84 4074.29 427.18 3553.62 5079.92 4848.24 4350.41 4002.13 5329.31 3919.06 4823.83 4488.31 627.07 -V80 2868.85 5047.99 6140.96 3806.85 7216.89 5022.46 5256.06 7169.93 5316.25 1519.33 6397.22 6182.99 4471.19 4996.46 5044.24 3879.66 5161.96 972.74 4630.92 5302.12 5241.23 6062.4 4313.43 6004.09 4748.38 3915.5 5027.26 767.88 -V81 1281.17 2380.08 2630.57 1937.7 2948.17 2691.06 2049.1 4141.95 2507.47 842.56 2926.15 2622.13 1919.88 2621.26 2455.64 2368.02 2485.52 336.42 2351.46 2619.77 3160.6 2527.13 2012.54 3985.57 2068.56 2219.55 2618.15 662.38 -V82 2146.74 3932.04 7069.54 3549.09 7827.98 6430.48 4776.82 6935.8 5333.56 2022.04 6914.18 5835.39 4308.74 5546.11 4125.61 3316.45 5007.75 1321.86 5274.98 6382.23 4334.58 7275.77 4046.02 6099.75 5484.72 2524.77 5177.85 1504.1 -V83 1907.68 3559.05 5257.18 3193.54 6000.27 5750.61 3999.64 7589.13 4657.14 1824.28 6055.9 5410.81 3697.01 5334.87 4176.24 3397.35 4678.7 1069.69 5656.93 5396.48 4561.55 5252.67 3739.43 5920.38 4914.96 2876.17 4789.82 1031.33 -V84 1563.87 3853.97 8432.18 3998.8 8762.48 7300.71 5457.68 7690.55 5882.53 2579.31 7568.64 6990.02 4975.96 6365.79 4614.85 3298.13 5635.56 1615.25 6009.26 8596.72 5386.72 9056.14 3895.21 8087.23 6738.97 2065.6 6229.48 2415.73 -V85 3302.09 7922.23 14839.62 8695.1 14895.67 16252.17 9849.17 16439.95 11524.5 4784.86 15467.28 13457.69 9570.14 14436.95 11137.53 7751.42 11970.17 2992.62 14886.11 19383.47 13977.26 15573.95 8041.42 19837.99 14672.95 5478.44 13981.45 4998.55 -V86 0 296.05 366.33 1166.3 169.79 130.5 910.02 161.2 400.02 414.37 118.7 194.08 229.06 300.62 98.91 317.51 209.81 90.62 117.23 575.01 90.37 827.4 371.26 112.71 288.72 0 297.84 283.19 -V87 4401.04 2934.89 3681.01 6152.67 2603.61 2332.57 5978.46 1842.04 3740.79 1638.59 2181.44 2571.46 2344.9 3162.33 1741.34 4144.96 2691.07 852.26 2984.39 3569.27 1848.09 3728.68 4482.7 3372.3 3045.7 5581.86 3576.62 1103.72 -V88 4420.06 1904.34 2745.79 4347.63 2944.8 1893.85 4677.78 1650.45 3073.09 1248.88 2285.76 1717.32 1691.2 1981.19 1265.7 3952.21 2148.9 946 1923.49 2689.61 1150.01 2382.48 3544.16 2397.09 2072.07 4295.69 2556.82 977.41 -V89 2025.01 1309.69 1534.02 1724.7 997.37 1112.13 1504.17 1062.01 1408.64 356.9 1060.36 1233.53 1053.84 1231.26 1037.81 1653.63 1211.74 234.19 1373.49 870.32 1061.5 971.79 1322.44 1953.7 1160.28 3600.17 1539.21 897.22 -V90 7867.46 4397.17 5500.73 6128.55 4480.76 4361.83 6223.22 3656.82 5327.07 1374.86 5401.66 4479.81 3795.24 4545.42 3955.3 6335.78 4752.2 958.89 5860.18 3637.58 3601.16 3030.4 5119.26 7934.1 3942.76 12438.43 5695.48 3154 -V91 15420.21 6374.06 8675.69 9187.97 9400.76 7612.14 11663.12 6741.51 9384.43 2960.52 10596.69 7079.71 6181.61 7096.04 6025.42 12463.24 8240.45 2652.77 9551.32 5992.62 5097.49 4421.58 9300.09 12959.02 6316.93 21213.88 9356.62 5563.45 -V92 6810.22 3429.58 4299.33 6127.84 4075.32 3344.66 5125.32 3028.74 4530.12 1375.11 4175.7 3140.88 3084.36 3031.18 2636.89 6669.27 3789.71 1500.91 3604.49 2605.3 2145.3 2993.63 4287.71 5353.81 3153.44 9144.78 4161.06 2250.33 -V93 0 354.36 350.3 379.16 287.08 292.88 444.09 303.69 301.44 132.41 207.65 392.54 274.35 267.83 257.3 382.95 297.1 74.08 238.86 145.6 268.33 189 452.98 351.16 243.21 1063.47 369.08 296.38 -V94 2856.36 2456.4 2540.2 3367.98 2179.99 1475.83 2299.58 2163.25 2417.45 552.18 1869.28 2155.91 1924.65 1709.17 1633.53 3130.02 2070.43 550.12 1852.97 935.78 2010.54 1819.26 2184.75 2451.9 1909.68 5332.67 2312.19 1296.17 -V95 24091.97 15443.29 15942.72 17970 12145.72 10870.02 14682.71 15930 15884.55 4008.56 13247.25 15454.42 13712.53 11623.37 9969.61 19752.29 13959.91 3398.12 9621.47 5782.84 11913.08 12015.65 12566.22 17116.78 13006.74 34928.36 14618.89 8804.83 -V96 60793.4 33382.53 33715.73 32764.43 24127.78 25432.17 29776.84 35260.09 34406.62 11394.51 28888.49 34024.7 31279.19 25136.41 21490.99 42646.24 30577.67 7389.9 16961.84 12299.55 24074.2 26183.98 25604.38 38438.79 28979.32 78126.8 31333.61 20446.85 -V97 17570.51 9240.64 9721.88 10284.94 6788.15 7088.16 9220.42 9323.72 9904.8 3334.56 7668.14 9513.44 7976.91 7000.53 6579.27 12453.69 8532 2170.52 4915.75 3693.18 6545.25 7271.72 7741.63 11272.66 8234.6 21625.05 8912.48 5612.76 -V98 0 149.15 135.65 144.37 124.09 117.76 110.31 127.3 113.58 47.7 128.4 127.61 126.27 136.02 105.67 160.41 130.73 17.73 118.88 107.55 121.9 120.41 133.07 129.53 119.35 0 106.34 43.64 -V99 314.71 233.89 257.32 290.71 136.54 131.91 212.71 151.12 216.11 70.67 144.84 161.98 199.1 177.26 109.83 276.15 178.19 56.71 136.06 92.56 133.57 240.27 196.46 181.17 175.41 0 144.44 73.62 -V100 1063.57 888.31 802.4 899.21 524.53 465.73 990.79 508.3 767.86 235.42 425.38 531.11 631.35 755.31 380.35 795.06 586.43 170.6 399.27 323.3 426.24 771.87 698.1 557.47 570.57 1826.56 696.67 480.86 -V101 2587.9 1673.54 1654.1 1984.41 1404.72 1474.72 2767.56 1490.35 1879.66 525.82 725.28 1591.13 1128.98 1962.5 1210.7 1571.45 1365.01 433.48 897.88 885.71 1024.88 1264.44 2472.8 1515.25 1349.88 4852 1782.85 1340.9 -V102 3565.72 1975.42 2013.22 2140.6 1668.46 2455.07 3602.33 2361.46 2472.79 726.93 769.9 2420.79 1099.54 1908.1 1814.65 1765.41 1629.73 596.03 990.98 1185.95 1435.53 1123.37 4179.54 2564.22 1660.72 6490.51 2453.85 1944.54 -V103 0 48.29 0 0 0 0 70.19 0 14.81 28.04 0 0 0 0 0 0 0 0 0 123.9 0 0 0 0 0 5.93 16.23 43.56 -V104 0 123.49 65.51 80.81 98.52 68.99 195.36 83.25 89.49 55.5 97.05 128.29 99.81 113.05 120.62 0 93.14 47.16 119.68 367.75 78.17 59.42 81.7 79.25 121.63 0 113.45 109.53 -V105 0 85.23 0 0 0 0 168.05 0 31.66 62.66 0 0 0 0 0 0 0 0 0 233.87 0 0 0 0 0 0 29.23 82.69 -V106 0 183.94 76.89 113 125.6 0 370.73 0 108.77 125.97 150.38 121.92 135.84 186.45 103.87 0 116.41 63.52 154.21 496.94 107.83 94.48 106.85 0 141.87 0 137.77 156.29 -V107 423.7 0 164.21 507.86 578.77 522.85 0 346.55 317.99 234.19 0 299.3 343.68 661.93 499.17 759.59 427.28 274.44 363.88 432.47 486.04 383.04 381.67 0 497.37 0 318.06 202.18 -V108 4.6 2.76 2.42 3.59 3.85 3.27 5.32 4.47 3.79 0.98 4.96 3.56 3.84 4.62 5.72 5.58 4.72 0.89 3.99 4.66 4.99 4.79 4.25 2.82 3.33 4.09 4.11 0.74 -V109 1.46 1.14 1.27 1.13 1.52 1.57 1.35 1.14 1.32 0.18 1.18 1.28 1.13 1.2 1.14 1.63 1.26 0.19 1.32 0.9 1.14 1.6 1.07 1.42 1.87 0.91 1.28 0.34 -V110 0.52 0.55 0 0.49 0 0 0 0.51 0.26 0.28 0.35 0.38 0.56 0.44 0 0.55 0.38 0.2 0.32 0.37 0.35 0.52 0 0.44 0.44 0.28 0.34 0.16 -V111 0.4 0 0 0.43 0.32 0 0 0.39 0.19 0.21 0.3 0.37 0 0.4 0 0.42 0.25 0.2 0 0.36 0.25 0.47 0 0.39 0.38 0 0.23 0.2 -V112 0.76 0.49 0.43 0.64 0.49 0.48 0.23 0.71 0.53 0.17 0.47 0.52 0.59 0.62 0.38 0.65 0.54 0.1 0.32 0.49 0.38 0.55 0.49 0.6 0.64 0.47 0.49 0.11 -V113 0.61 0.58 0.53 0.53 0.45 0.31 0.15 0.51 0.46 0.15 0.36 0.51 0.44 0.45 0.48 0.66 0.48 0.1 0.33 0.53 0.37 0.61 0.36 0.51 0.67 0.33 0.46 0.13 -V114 0 0 0 0 0.09 0 0 0.12 0.03 0.05 0 0.1 0 0 0 0 0.02 0.04 0 0 0.1 0 0.12 0.11 0 0 0.04 0.06 -V115 0 0 0 0 0 0 0 0.13 0.02 0.04 0 0.11 0 0 0 0 0.02 0.05 0 0 0 0 0.15 0.12 0 0 0.03 0.06 -V116 1.76 1.89 1.43 1.19 1.34 1.64 0 2.33 1.44 0.68 1.16 2.16 0 1.74 2.23 1.12 1.4 0.83 0 1.47 1.37 1.34 2.27 1.83 1.51 1.43 1.4 0.65 diff -r ad06aeed02c9 -r db1d80e89156 tests/exa2/sampleMetadata.tsv --- a/tests/exa2/sampleMetadata.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -sampleMetadata meta1 -S1 A -S2 A -S3 A -S4 A -S5 A -S6 A -S7 A -S8 A -S9 B -S10 B -S11 B -S12 B -S13 B -S14 B -S15 B -S16 C -S17 C -S18 C -S19 C -S20 C -S21 C -S22 C -S23 C -S24 C -S25 BC -S26 AB -S27 BC -S28 AC diff -r ad06aeed02c9 -r db1d80e89156 tests/exa2/variableMetadata.tsv --- a/tests/exa2/variableMetadata.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,117 +0,0 @@ -variableMetadata meta2 -V1 ER -V2 GGG -V3 GGG -V4 GGG -V5 GGG -V6 CE -V7 CE -V8 CE -V9 TG -V10 TG -V11 TG -V12 TG -V13 TG -V14 AM -V15 AM -V16 AM -V17 AM -V18 AM -V19 AM -V20 AM -V21 AM -V22 AM -V23 AM -V24 AM -V25 AM -V26 AM -V27 AM -V28 AM -V29 AM -V30 AM -V31 AM -V32 ER -V33 ER -V34 ER -V35 ER -V36 ER -V37 CER -V38 CER -V39 CER -V40 CER -V41 CER -V42 CER -V43 CER -V44 CER -V45 CER -V46 CER -V47 PP -V48 PP -V49 PP -V50 PP -V51 PP -V52 PP -V53 PP -V54 PP -V55 PP -V56 PP -V57 PP -V58 PP -V59 PP -V60 PP -V61 PP -V62 PP -V63 PP -V64 CC -V65 CC -V66 CC -V67 CC -V68 CC -V69 CC -V70 CC -V71 CC -V72 CC -V73 CC -V74 CC -V75 CC -V76 CC -V77 CC -V78 CC -V79 CC -V80 CC -V81 CC -V82 CC -V83 CC -V84 CC -V85 SM -V86 SM -V87 SM -V88 SM -V89 SM -V90 SM -V91 SM -V92 SM -V93 SM -V94 SM -V95 SM -V96 PI -V97 PI -V98 PI -V99 PI -V100 PI -V101 PI -V102 PI -V103 PI -V104 PI -V105 PI -V106 PI -V107 NG -V108 NG -V109 NG -V110 SO -V111 SO -V112 SO -V113 SO -V114 SO -V115 SO -V116 SO diff -r ad06aeed02c9 -r db1d80e89156 tests/heatmap_runtests.R --- a/tests/heatmap_runtests.R Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -#!/usr/bin/env Rscript - -## Package -##-------- - -library(RUnit) - -## Constants -##---------- - -testOutDirC <- "output" -argVc <- commandArgs(trailingOnly = FALSE) -scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)]) - - -## Functions -##----------- - -## Reading tables (matrix or data frame) -readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) { - - file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\".")) - - switch(typeC, - matrix = return(t(as.matrix(read.table(file = fileC, - header = TRUE, - row.names = 1, - sep = "\t", - stringsAsFactors = FALSE)))), - dataframe = return(read.table(file = fileC, - header = TRUE, - row.names = 1, - sep = "\t", - stringsAsFactors = FALSE))) - -} - -## Call wrapper -wrapperCallF <- function(paramLs) { - - ## Set program path - wrapperPathC <- file.path(dirname(scriptPathC), "..", "heatmap_wrapper.R") - - ## Set arguments - argLs <- NULL - for (parC in names(paramLs)) - argLs <- c(argLs, parC, paramLs[[parC]]) - - ## Call - wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ") - - if(.Platform$OS.type == "windows") - wrapperCallC <- paste("Rscript", wrapperCallC) - - wrapperCodeN <- system(wrapperCallC) - - if (wrapperCodeN != 0) - stop("Error when running heatmap_wrapper.R.") - - ## Get output - outLs <- list() - if ("dataMatrix_out" %in% names(paramLs)) - outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix") - if ("sampleMetadata_out" %in% names(paramLs)) - outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe") - if ("variableMetadata_out" %in% names(paramLs)) - outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe") - if("information" %in% names(paramLs)) - outLs[["infVc"]] <- readLines(paramLs[["information"]]) - - return(outLs) -} - -## Setting default parameters -defaultArgF <- function(testInDirC) { - - defaultArgLs <- list() - if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv"))) - defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv") - if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv"))) - defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv") - if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv"))) - defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv") - - defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv") - defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv") - defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv") - defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf") - defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt") - - defaultArgLs - -} - -## Main -##----- - -## Create output folder -file.exists(testOutDirC) || dir.create(testOutDirC) - -## Run tests -test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$') -isValidTestSuite(test.suite) -test.results <- runTestSuite(test.suite) -print(test.results) diff -r ad06aeed02c9 -r db1d80e89156 tests/heatmap_tests.R --- a/tests/heatmap_tests.R Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -test_input_cut4 <- function() { - - testDirC <- "input" - argLs <- list(disC = "1-cor", - cutSamN = "4", - cutVarN = "3", - corMetC = "spearman", - aggMetC = "ward", - colC = "blueOrangeRed", - scaL = "TRUE", - cexN = "0.8") - - argLs <- c(defaultArgF(testDirC), argLs) - outLs <- wrapperCallF(argLs) - - checkEqualsNumeric(outLs[['samDF']][13, 'heat_clust'], 4) - -} - -test_exa1_cut3 <- function() { - - testDirC <- "exa1" - argLs <- list(disC = "1-cor", - cutSamN = "3", - cutVarN = "4", - corMetC = "spearman", - aggMetC = "ward", - colC = "blueOrangeRed", - scaL = "TRUE", - cexN = "1") - - argLs <- c(defaultArgF(testDirC), argLs) - outLs <- wrapperCallF(argLs) - - checkEqualsNumeric(outLs[['varDF']]['V24', 'heat_clust'], 4) - -} - -test_exa2_cut4 <- function() { - - testDirC <- "exa2" - argLs <- list(disC = "1-cor", - cutSamN = "1", - cutVarN = "1", - corMetC = "spearman", - aggMetC = "ward", - colC = "blueOrangeRed", - scaL = "TRUE", - cexN = "1") - - argLs <- c(defaultArgF(testDirC), argLs) - outLs <- wrapperCallF(argLs) - - checkEquals(outLs[['varDF']]['V31', 'meta2'], 'AM') - -} - diff -r ad06aeed02c9 -r db1d80e89156 tests/input/dataMatrix.tsv --- a/tests/input/dataMatrix.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 -HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 -HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 32742 -HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 1580343 39315 -HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 994336 239030 -HMDB00822 483755 579287 1132413 157113 1577570 1469735 1085454 477909 814755 245417 610681 763706 2406336 827531 992508 569605 355321 150259 1334200 271010 -HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 1517319 841661 -HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 1992420 284775 -HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 1061418 622898 -HMDB00518 34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 867108 73831 -HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 7517724 1341900 -HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 9120781 44276 -HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 3359238 2540044 -HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 1824553 387811 -HMDB00512 53304 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 438839 85554 -HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 454489 616061 diff -r ad06aeed02c9 -r db1d80e89156 tests/input/sampleMetadata.tsv --- a/tests/input/sampleMetadata.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender -HU_017 2 pos 41 23.03 M -HU_028 7 pos 41 23.92 F -HU_034 9 pos 52 23.37 M -HU_051 20 pos 24 23.23 F -HU_060 24 pos 55 28.72 F -HU_078 34 pos 46 25.18 M -HU_091 42 pos 61 26.12 M -HU_093 43 pos 53 21.71 M -HU_099 46 pos 23 21.3 M -HU_110 53 pos 50 20.9 F -HU_130 63 pos 33 26.06 M -HU_134 67 pos 48 22.89 M -HU_138 68 pos 42 21.88 M -HU_149 72 pos 35 19.49 F -HU_152 75 pos 26 17.58 F -HU_175 87 pos 35 21.26 F -HU_178 88 pos 60 32.87 F -HU_185 95 pos 42 21.09 F -HU_204 104 pos 31 29.06 M -HU_208 106 pos 27 18.61 F diff -r ad06aeed02c9 -r db1d80e89156 tests/input/variableMetadata.tsv --- a/tests/input/variableMetadata.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -variableMetadata name -HMDB03193 Testosterone_glucuronide -HMDB01101 p-Anisic_acid -HMDB10348 Dehydroepiandrosterone_3-glucuronide -HMDB59717 Glu-Val -HMDB00822 p-Hydroxymandelic_acid -HMDB13189 3-Indole_carboxylic_acid_glucuronide -HMDB00299 Xanthosine -HMDB00191 L-Aspartic_acid -HMDB00518 Chenodeoxycholic_acid -HMDB00715 Kynurenic_acid -HMDB01032 Dehydroepiandrosterone_sulfate -HMDB00208 Oxoglutaric_acid -HMDB04824 N2,N2-Dimethylguanosine -HMDB00512 N-Acetyl-L-phenylalanine -HMDB00251 Taurine diff -r ad06aeed02c9 -r db1d80e89156 tests/output/dataMatrix.tsv --- a/tests/output/dataMatrix.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -dataMatrix HU_051 HU_208 HU_178 HU_130 HU_175 HU_099 HU_152 HU_204 HU_017 HU_138 HU_034 HU_078 HU_060 HU_149 HU_028 HU_093 HU_134 HU_091 HU_110 HU_185 -HMDB13189 619181 841661 2092753 1608814 2893445 3526136 3132404 1517319 2644620 1941527 1661412 2755434 136278 113937 727587 837865 3446611 593863 2003278 1034666 -HMDB00251 622468 616061 80614 310918 403815 268331 335711 454489 368600 577184 94936 293988 180988 10985 616555 767894 1248919 352855 167246 63393 -HMDB01101 3158 32742 31250 608298 1464339 976436 1107705 72900 30689 72021 52217 229568 10789748 442510 6877586 3878773 1605075 4763576 831937 2724553 -HMDB00191 392284 622898 710519 639437 1945577 960658 1246459 1061418 560002 1409045 575790 785428 888498 2292023 771533 591569 1092885 645785 910201 773384 -HMDB00208 1172376 2540044 7037373 2477288 10335722 5593888 8960828 3359238 747080 4230072 595872 3143654 7172632 7621236 13420742 1433702 3346077 4059767 5402629 1574738 -HMDB59717 67604 239030 784738 808334 1563158 1378535 715190 994336 357351 871209 301983 1028110 306862 895435 1030464 270027 1132813 1530493 289677 146195 -HMDB00512 85009 85554 827723 569970 1171008 342532 542345 438839 53304 246282 280560 556003 1333877 1140422 319783 209285 525240 590779 198512 222953 -HMDB00518 NA 73831 514579 440223 28361 230242 48673 867108 34236 10657 85944 129886 342102 419508 58249 13154 315368 175800 NA 23108 -HMDB00822 157113 271010 355321 610681 569605 814755 992508 1334200 483755 2406336 1132413 1469735 1577570 827531 579287 477909 763706 1085454 245417 150259 -HMDB00715 371059 1341900 2295288 4184204 3577833 2558923 3820724 7517724 1252089 3236644 905408 5140022 4983588 2615560 2547452 814523 3865723 2658555 859466 625924 -HMDB01032 430453 44276 871010 31151730 5588731 59906109 20249262 9120781 2569205 14989438 1604999 26222916 8103558 1554658 26023086 675754 18648127 257139 263055 15920 -HMDB00299 159386 284775 411886 504108 566050 768004 1110050 1992420 250551 1362408 456162 808657 1013302 1057660 1046138 250403 1014041 614370 242085 142233 -HMDB04824 178517 387811 782673 477995 1020206 1253319 1411802 1824553 374028 1157093 539206 959381 1046190 1089284 1144386 310260 825691 605191 477259 346761 -HMDB03193 27242 43907 79673 339188 212500 559869 451270 891129 76043 262271 44943 173175 436566 127285 412165 57066 471368 242549 3732 NA -HMDB10348 34582 39315 214392 279156 161069 610110 433529 1580343 47259 451573 60885 168264 529874 591487 544877 76457 524468 176500 16262 13781 diff -r ad06aeed02c9 -r db1d80e89156 tests/output/essai.tsv --- a/tests/output/essai.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender heat_clust -HU_017 2 pos 41 23.03 M 1 -HU_034 9 pos 52 23.37 M 1 -HU_204 104 pos 31 29.06 M 2 -HU_134 67 pos 48 22.89 M 2 -HU_099 46 pos 23 21.3 M 2 -HU_078 34 pos 46 25.18 M 2 -HU_130 63 pos 33 26.06 M 2 -HU_028 7 pos 41 23.92 F 2 -HU_138 68 pos 42 21.88 M 2 -HU_152 75 pos 26 17.58 F 2 -HU_051 20 pos 24 23.23 F 3 -HU_208 106 pos 27 18.61 F 3 -HU_110 53 pos 50 20.9 F 3 -HU_178 88 pos 60 32.87 F 3 -HU_149 72 pos 35 19.49 F 3 -HU_175 87 pos 35 21.26 F 3 -HU_060 24 pos 55 28.72 F 4 -HU_091 42 pos 61 26.12 M 4 -HU_093 43 pos 53 21.71 M 4 -HU_185 95 pos 42 21.09 F 4 diff -r ad06aeed02c9 -r db1d80e89156 tests/output/figure.pdf Binary file tests/output/figure.pdf has changed diff -r ad06aeed02c9 -r db1d80e89156 tests/output/information.txt --- a/tests/output/information.txt Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ - -Start of the 'Heatmap' module: Tue 02 Aug 2016 11:48:22 AM - -Arguments used: - - value -dataMatrix_in "tests/input/dataMatrix.tsv" -sampleMetadata_in "tests/input/sampleMetadata.tsv" -variableMetadata_in "tests/input/variableMetadata.tsv" -dataMatrix_out "tests/output/dataMatrix.tsv" -sampleMetadata_out "tests/output/sampleMetadata.tsv" -variableMetadata_out "tests/output/variableMetadata.tsv" -figure "tests/output/figure.pdf" -information "tests/output/information.txt" -disC "1-cor" -cutSamN "4" -cutVarN "3" -corMetC "spearman" -aggMetC "ward" -colC "blueOrangeRed" -scaL "TRUE" -cexN "0.8" - -End of the 'Heatmap' Galaxy module call: Tue 02 Aug 2016 11:48:22 AM diff -r ad06aeed02c9 -r db1d80e89156 tests/output/sampleMetadata.tsv --- a/tests/output/sampleMetadata.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -sampleMetadata injectionOrder mode age bmi gender heat_clust -HU_051 20 pos 24 23.23 F 3 -HU_208 106 pos 27 18.61 F 3 -HU_178 88 pos 60 32.87 F 1 -HU_130 63 pos 33 26.06 M 1 -HU_175 87 pos 35 21.26 F 1 -HU_099 46 pos 23 21.3 M 1 -HU_152 75 pos 26 17.58 F 1 -HU_204 104 pos 31 29.06 M 1 -HU_017 2 pos 41 23.03 M 1 -HU_138 68 pos 42 21.88 M 1 -HU_034 9 pos 52 23.37 M 1 -HU_078 34 pos 46 25.18 M 1 -HU_060 24 pos 55 28.72 F 4 -HU_149 72 pos 35 19.49 F 4 -HU_028 7 pos 41 23.92 F 2 -HU_093 43 pos 53 21.71 M 2 -HU_134 67 pos 48 22.89 M 2 -HU_091 42 pos 61 26.12 M 2 -HU_110 53 pos 50 20.9 F 2 -HU_185 95 pos 42 21.09 F 2 diff -r ad06aeed02c9 -r db1d80e89156 tests/output/variableMetadata.tsv --- a/tests/output/variableMetadata.tsv Tue Aug 02 06:26:41 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -variableMetadata name heat_clust -HMDB13189 3-Indole_carboxylic_acid_glucuronide 3 -HMDB00251 Taurine 3 -HMDB01101 p-Anisic_acid 2 -HMDB00191 L-Aspartic_acid 2 -HMDB00208 Oxoglutaric_acid 2 -HMDB59717 Glu-Val 2 -HMDB00512 N-Acetyl-L-phenylalanine 2 -HMDB00518 Chenodeoxycholic_acid 1 -HMDB00822 p-Hydroxymandelic_acid 1 -HMDB00715 Kynurenic_acid 1 -HMDB01032 Dehydroepiandrosterone_sulfate 1 -HMDB00299 Xanthosine 1 -HMDB04824 N2,N2-Dimethylguanosine 1 -HMDB03193 Testosterone_glucuronide 1 -HMDB10348 Dehydroepiandrosterone_3-glucuronide 1