| Previous changeset 0:ad06aeed02c9 (2016-08-02) Next changeset 2:b1667c118127 (2017-06-06) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 29f9ccf5bd558becff5913528bb998aa7bb82d44 |
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modified:
README.md heatmap_config.xml |
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added:
runit/exa1/dataMatrix.tsv runit/exa1/sampleMetadata.tsv runit/exa1/variableMetadata.tsv runit/exa2/dataMatrix.tsv runit/exa2/sampleMetadata.tsv runit/exa2/variableMetadata.tsv runit/heatmap_runtests.R runit/heatmap_tests.R runit/input/dataMatrix.tsv runit/input/sampleMetadata.tsv runit/input/variableMetadata.tsv runit/output/dataMatrix.tsv runit/output/essai.tsv runit/output/figure.pdf runit/output/information.txt runit/output/sampleMetadata.tsv runit/output/variableMetadata.tsv |
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removed:
tests/exa1/dataMatrix.tsv tests/exa1/sampleMetadata.tsv tests/exa1/variableMetadata.tsv tests/exa2/dataMatrix.tsv tests/exa2/sampleMetadata.tsv tests/exa2/variableMetadata.tsv tests/heatmap_runtests.R tests/heatmap_tests.R tests/input/dataMatrix.tsv tests/input/sampleMetadata.tsv tests/input/variableMetadata.tsv tests/output/dataMatrix.tsv tests/output/essai.tsv tests/output/figure.pdf tests/output/information.txt tests/output/sampleMetadata.tsv tests/output/variableMetadata.tsv |
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| 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 |
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| @@ -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: [](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 |
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| 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 |
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| @@ -1,13 +1,18 @@ -<tool id="Heatmap" name="Heatmap" version="2.2.0"> +<tool id="Heatmap" name="Heatmap" version="2.2.2"> <description>Heatmap of the dataMatrix</description> <requirements> <requirement type="package" version="3.2.2">R</requirement> <requirement type="package">r-batch</requirement> </requirements> - + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <command><![CDATA[ Rscript $__tool_directory__/heatmap_wrapper.R + dataMatrix_in "$dataMatrix_in" sampleMetadata_in "$sampleMetadata_in" variableMetadata_in "$variableMetadata_in" @@ -292,7 +297,7 @@ .. class:: infomark -See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu +See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) --------------------------------------------------- @@ -300,6 +305,13 @@ NEWS ---- +CHANGES IN VERSION 2.2.2 +======================== + +INTERNAL MODIFICATIONS + +Minor internal modifications + CHANGES IN VERSION 2.2.0 ======================== @@ -322,11 +334,21 @@ CHANGES IN VERSION 2.1.1 ======================== +INTERNAL MODIFICATIONS + Internal replacement of the as.hclust function which happened to produce error messages </help> <citations> + <citation type="bibtex">@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/}, + }</citation> <citation type="bibtex">@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} - }</citation> + }</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> </tool> |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| b'@@ -0,0 +1,117 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|
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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) |
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| 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') + +} + |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| diff -r ad06aeed02c9 -r db1d80e89156 runit/output/figure.pdf |
| b |
| Binary file runit/output/figure.pdf has changed |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| b'@@ -1,117 +0,0 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t2417.45\t552.18\t1869.28\t2155.91\t1924.65\t1709.17\t1633.53\t3130.02\t2070.43\t550.12\t1852.97\t935.78\t2010.54\t1819.26\t2184.75\t2451.9\t1909.68\t5332.67\t2312.19\t1296.17\n-V95\t24091.97\t15443.29\t15942.72\t17970\t12145.72\t10870.02\t14682.71\t15930\t15884.55\t4008.56\t13247.25\t15454.42\t13712.53\t11623.37\t9969.61\t19752.29\t13959.91\t3398.12\t9621.47\t5782.84\t11913.08\t12015.65\t12566.22\t17116.78\t13006.74\t34928.36\t14618.89\t8804.83\n-V96\t60793.4\t33382.53\t33715.73\t32764.43\t24127.78\t25432.17\t29776.84\t35260.09\t34406.62\t11394.51\t28888.49\t34024.7\t31279.19\t25136.41\t21490.99\t42646.24\t30577.67\t7389.9\t16961.84\t12299.55\t24074.2\t26183.98\t25604.38\t38438.79\t28979.32\t78126.8\t31333.61\t20446.85\n-V97\t17570.51\t9240.64\t9721.88\t10284.94\t6788.15\t7088.16\t9220.42\t9323.72\t9904.8\t3334.56\t7668.14\t9513.44\t7976.91\t7000.53\t6579.27\t12453.69\t8532\t2170.52\t4915.75\t3693.18\t6545.25\t7271.72\t7741.63\t11272.66\t8234.6\t21625.05\t8912.48\t5612.76\n-V98\t0\t149.15\t135.65\t144.37\t124.09\t117.76\t110.31\t127.3\t113.58\t47.7\t128.4\t127.61\t126.27\t136.02\t105.67\t160.41\t130.73\t17.73\t118.88\t107.55\t121.9\t120.41\t133.07\t129.53\t119.35\t0\t106.34\t43.64\n-V99\t314.71\t233.89\t257.32\t290.71\t136.54\t131.91\t212.71\t151.12\t216.11\t70.67\t144.84\t161.98\t199.1\t177.26\t109.83\t276.15\t178.19\t56.71\t136.06\t92.56\t133.57\t240.27\t196.46\t181.17\t175.41\t0\t144.44\t73.62\n-V100\t1063.57\t888.31\t802.4\t899.21\t524.53\t465.73\t990.79\t508.3\t767.86\t235.42\t425.38\t531.11\t631.35\t755.31\t380.35\t795.06\t586.43\t170.6\t399.27\t323.3\t426.24\t771.87\t698.1\t557.47\t570.57\t1826.56\t696.67\t480.86\n-V101\t2587.9\t1673.54\t1654.1\t1984.41\t1404.72\t1474.72\t2767.56\t1490.35\t1879.66\t525.82\t725.28\t1591.13\t1128.98\t1962.5\t1210.7\t1571.45\t1365.01\t433.48\t897.88\t885.71\t1024.88\t1264.44\t2472.8\t1515.25\t1349.88\t4852\t1782.85\t1340.9\n-V102\t3565.72\t1975.42\t2013.22\t2140.6\t1668.46\t2455.07\t3602.33\t2361.46\t2472.79\t726.93\t769.9\t2420.79\t1099.54\t1908.1\t1814.65\t1765.41\t1629.73\t596.03\t990.98\t1185.95\t1435.53\t1123.37\t4179.54\t2564.22\t1660.72\t6490.51\t2453.85\t1944.54\n-V103\t0\t48.29\t0\t0\t0\t0\t70.19\t0\t14.81\t28.04\t0\t0\t0\t0\t0\t0\t0\t0\t0\t123.9\t0\t0\t0\t0\t0\t5.93\t16.23\t43.56\n-V104\t0\t123.49\t65.51\t80.81\t98.52\t68.99\t195.36\t83.25\t89.49\t55.5\t97.05\t128.29\t99.81\t113.05\t120.62\t0\t93.14\t47.16\t119.68\t367.75\t78.17\t59.42\t81.7\t79.25\t121.63\t0\t113.45\t109.53\n-V105\t0\t85.23\t0\t0\t0\t0\t168.05\t0\t31.66\t62.66\t0\t0\t0\t0\t0\t0\t0\t0\t0\t233.87\t0\t0\t0\t0\t0\t0\t29.23\t82.69\n-V106\t0\t183.94\t76.89\t113\t125.6\t0\t370.73\t0\t108.77\t125.97\t150.38\t121.92\t135.84\t186.45\t103.87\t0\t116.41\t63.52\t154.21\t496.94\t107.83\t94.48\t106.85\t0\t141.87\t0\t137.77\t156.29\n-V107\t423.7\t0\t164.21\t507.86\t578.77\t522.85\t0\t346.55\t317.99\t234.19\t0\t299.3\t343.68\t661.93\t499.17\t759.59\t427.28\t274.44\t363.88\t432.47\t486.04\t383.04\t381.67\t0\t497.37\t0\t318.06\t202.18\n-V108\t4.6\t2.76\t2.42\t3.59\t3.85\t3.27\t5.32\t4.47\t3.79\t0.98\t4.96\t3.56\t3.84\t4.62\t5.72\t5.58\t4.72\t0.89\t3.99\t4.66\t4.99\t4.79\t4.25\t2.82\t3.33\t4.09\t4.11\t0.74\n-V109\t1.46\t1.14\t1.27\t1.13\t1.52\t1.57\t1.35\t1.14\t1.32\t0.18\t1.18\t1.28\t1.13\t1.2\t1.14\t1.63\t1.26\t0.19\t1.32\t0.9\t1.14\t1.6\t1.07\t1.42\t1.87\t0.91\t1.28\t0.34\n-V110\t0.52\t0.55\t0\t0.49\t0\t0\t0\t0.51\t0.26\t0.28\t0.35\t0.38\t0.56\t0.44\t0\t0.55\t0.38\t0.2\t0.32\t0.37\t0.35\t0.52\t0\t0.44\t0.44\t0.28\t0.34\t0.16\n-V111\t0.4\t0\t0\t0.43\t0.32\t0\t0\t0.39\t0.19\t0.21\t0.3\t0.37\t0\t0.4\t0\t0.42\t0.25\t0.2\t0\t0.36\t0.25\t0.47\t0\t0.39\t0.38\t0\t0.23\t0.2\n-V112\t0.76\t0.49\t0.43\t0.64\t0.49\t0.48\t0.23\t0.71\t0.53\t0.17\t0.47\t0.52\t0.59\t0.62\t0.38\t0.65\t0.54\t0.1\t0.32\t0.49\t0.38\t0.55\t0.49\t0.6\t0.64\t0.47\t0.49\t0.11\n-V113\t0.61\t0.58\t0.53\t0.53\t0.45\t0.31\t0.15\t0.51\t0.46\t0.15\t0.36\t0.51\t0.44\t0.45\t0.48\t0.66\t0.48\t0.1\t0.33\t0.53\t0.37\t0.61\t0.36\t0.51\t0.67\t0.33\t0.46\t0.13\n-V114\t0\t0\t0\t0\t0.09\t0\t0\t0.12\t0.03\t0.05\t0\t0.1\t0\t0\t0\t0\t0.02\t0.04\t0\t0\t0.1\t0\t0.12\t0.11\t0\t0\t0.04\t0.06\n-V115\t0\t0\t0\t0\t0\t0\t0\t0.13\t0.02\t0.04\t0\t0.11\t0\t0\t0\t0\t0.02\t0.05\t0\t0\t0\t0\t0.15\t0.12\t0\t0\t0.03\t0.06\n-V116\t1.76\t1.89\t1.43\t1.19\t1.34\t1.64\t0\t2.33\t1.44\t0.68\t1.16\t2.16\t0\t1.74\t2.23\t1.12\t1.4\t0.83\t0\t1.47\t1.37\t1.34\t2.27\t1.83\t1.51\t1.43\t1.4\t0.65\n' |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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) |
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| 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 |
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| @@ -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') - -} - |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| diff -r ad06aeed02c9 -r db1d80e89156 tests/output/figure.pdf |
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| Binary file tests/output/figure.pdf has changed |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |