Mercurial > repos > ethevenot > univariate

annotate univariate_script.R @ 0:ab2ee3414e4e draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
author ethevenot
date Tue, 24 Oct 2017 08:57:25 -0400
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
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diff changeset
1 univariateF <- function(datMN,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
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2 samDF,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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3 varDF,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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4 facC,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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5 tesC = c("ttest", "wilcoxon", "anova", "kruskal", "pearson", "spearman")[1],
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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6 adjC = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")[7],
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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7 thrN = 0.05,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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8 pdfC) {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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11 ## Option
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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13 strAsFacL <- options()$stringsAsFactors
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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14 options(stingsAsFactors = FALSE)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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15 options(warn = -1)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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17 ## Getting the response (either a factor or a numeric)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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19 if(mode(samDF[, facC]) == "character") {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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20 facFcVn <- factor(samDF[, facC])
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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21 facLevVc <- levels(facFcVn)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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22 } else
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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23 facFcVn <- samDF[, facC]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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25 cat("\nPerforming '", tesC, "'\n", sep="")
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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27 varPfxC <- paste0(make.names(facC), "_", tesC, "_")
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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30 if(tesC %in% c("ttest", "wilcoxon", "pearson", "spearman")) {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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32
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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33 switch(tesC,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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34 ttest = {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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35 staF <- function(y) diff(tapply(y, facFcVn, function(x) mean(x, na.rm = TRUE)))
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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36 tesF <- function(y) t.test(y ~ facFcVn)[["p.value"]]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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37 },
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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38 wilcoxon = {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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39 staF <- function(y) diff(tapply(y, facFcVn, function(x) median(x, na.rm = TRUE)))
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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40 tesF <- function(y) wilcox.test(y ~ facFcVn)[["p.value"]]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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41 },
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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42 pearson = {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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43 staF <- function(y) cor(facFcVn, y, method = "pearson", use = "pairwise.complete.obs")
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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44 tesF <- function(y) cor.test(facFcVn, y, method = "pearson", use = "pairwise.complete.obs")[["p.value"]]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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45 },
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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46 spearman = {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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47 staF <- function(y) cor(facFcVn, y, method = "spearman", use = "pairwise.complete.obs")
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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48 tesF <- function(y) cor.test(facFcVn, y, method = "spearman", use = "pairwise.complete.obs")[["p.value"]]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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49 })
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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50
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51 staVn <- apply(datMN, 2, staF)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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52
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53 adjVn <- p.adjust(apply(datMN,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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54 2,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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55 tesF),
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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56 method = adjC)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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57
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58 sigVn <- as.numeric(adjVn < thrN)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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59
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60 if(tesC %in% c("ttest", "wilcoxon"))
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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61 varPfxC <- paste0(varPfxC, paste(rev(facLevVc), collapse = "."), "_")
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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62
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63 varDF[, paste0(varPfxC, ifelse(tesC %in% c("ttest", "wilcoxon"), "dif", "cor"))] <- staVn
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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64
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65 varDF[, paste0(varPfxC, adjC)] <- adjVn
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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66
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67 varDF[, paste0(varPfxC, "sig")] <- sigVn
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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68
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69 ## graphic
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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70
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71 pdf(pdfC, onefile = TRUE)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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72
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73 varVi <- which(sigVn > 0)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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74
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75 if(tesC %in% c("ttest", "wilcoxon")) {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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76
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77 facVc <- as.character(facFcVn)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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78 names(facVc) <- rownames(samDF)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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79
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80 for(varI in varVi) {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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81
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82 varC <- rownames(varDF)[varI]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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83
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84 boxF(facFcVn,
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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85 datMN[, varI],
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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86 paste0(varC, " (", adjC, " = ", signif(adjVn[varI], 2), ")"),
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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87 facVc)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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88
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89 }
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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90
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91 } else { ## pearson or spearman
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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92
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93 for(varI in varVi) {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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94
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95 varC <- rownames(varDF)[varI]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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96
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97 mod <- lm(datMN[, varI] ~ facFcVn)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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98
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99 plot(facFcVn, datMN[, varI],
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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100 xlab = facC,
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101 ylab = "",
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102 pch = 18,
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103 main = paste0(varC, " (", adjC, " = ", signif(adjVn[varI], 2), ", R2 = ", signif(summary(mod)$r.squared, 2), ")"))
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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104
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105 abline(mod, col = "red")
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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106
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107 }
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108
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109 }
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110
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111 dev.off()
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112
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113
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114 } else if(tesC == "anova") {
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115
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116
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117 ## getting the names of the pairwise comparisons 'class1Vclass2'
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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118 prwVc <- rownames(TukeyHSD(aov(datMN[, 1] ~ facFcVn))[["facFcVn"]])
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119
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120 prwVc <- gsub("-", ".", prwVc, fixed = TRUE) ## 2016-08-05: '-' character in dataframe column names seems not to be converted to "." by write.table on ubuntu R-3.3.1
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121
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122 ## omnibus and post-hoc tests
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123
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124 aovMN <- t(apply(datMN, 2, function(varVn) {
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125
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126 aovMod <- aov(varVn ~ facFcVn)
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127 pvaN <- summary(aovMod)[[1]][1, "Pr(>F)"]
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128 hsdMN <- TukeyHSD(aovMod)[["facFcVn"]]
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129 c(pvaN, c(hsdMN[, c("diff", "p adj")]))
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130
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131 }))
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132
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133 difVi <- 1:length(prwVc) + 1
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134
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135 ## difference of the means for each pairwise comparison
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136
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137 difMN <- aovMN[, difVi]
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138 colnames(difMN) <- paste0(varPfxC, prwVc, "_dif")
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139
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140 ## correction for multiple testing
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141
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142 aovMN <- aovMN[, -difVi, drop = FALSE]
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143 aovMN <- apply(aovMN, 2, function(pvaVn) p.adjust(pvaVn, method = adjC))
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144
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145 ## significance coding (0 = not significant, 1 = significant)
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146
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147 adjVn <- aovMN[, 1]
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148 sigVn <- as.numeric(adjVn < thrN)
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149
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150 aovMN <- aovMN[, -1, drop = FALSE]
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151 colnames(aovMN) <- paste0(varPfxC, prwVc, "_", adjC)
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152
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153 aovSigMN <- aovMN < thrN
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154 mode(aovSigMN) <- "numeric"
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155 colnames(aovSigMN) <- paste0(varPfxC, prwVc, "_sig")
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156
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157 ## final aggregated table
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158
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159 resMN <- cbind(adjVn, sigVn, difMN, aovMN, aovSigMN)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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160 colnames(resMN)[1:2] <- paste0(varPfxC, c(adjC, "sig"))
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161
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162 varDF <- cbind.data.frame(varDF, as.data.frame(resMN))
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163
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164 ## graphic
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165
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166 pdf(pdfC, onefile = TRUE)
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167
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168 for(varI in 1:nrow(varDF)) {
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169
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170 if(sum(aovSigMN[varI, ]) > 0) {
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171
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172 varC <- rownames(varDF)[varI]
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173
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174 boxplot(datMN[, varI] ~ facFcVn,
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175 main = paste0(varC, " (", adjC, " = ", signif(adjVn[varI], 2), ")"))
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176
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177 for(prwI in 1:length(prwVc)) {
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178
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179 if(aovSigMN[varI, paste0(varPfxC, prwVc[prwI], "_sig")] == 1) {
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180
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181 claVc <- unlist(strsplit(prwVc[prwI], ".", fixed = TRUE))
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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182 aovClaVl <- facFcVn %in% claVc
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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183 aovFc <- facFcVn[aovClaVl, drop = TRUE]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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184 aovVc <- as.character(aovFc)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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185 names(aovVc) <- rownames(samDF)[aovClaVl]
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186 boxF(aovFc,
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187 datMN[aovClaVl, varI],
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188 paste0(varC, " (", adjC, " = ", signif(aovMN[varI, paste0(varPfxC, prwVc[prwI], "_", adjC)], 2), ")"),
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189 aovVc)
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190
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191 }
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192
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193 }
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194
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195 }
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196
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197 }
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198
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199 dev.off()
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200
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201
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202 } else if(tesC == "kruskal") {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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203
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204
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205 ## getting the names of the pairwise comparisons 'class1.class2'
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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206
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207 nemMN <- posthoc.kruskal.nemenyi.test(datMN[, 1], facFcVn, "Tukey")[["p.value"]]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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208 nemVl <- c(lower.tri(nemMN, diag = TRUE))
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209 nemClaMC <- cbind(rownames(nemMN)[c(row(nemMN))][nemVl],
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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210 colnames(nemMN)[c(col(nemMN))][nemVl])
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211 nemNamVc <- paste0(nemClaMC[, 1], ".", nemClaMC[, 2])
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212 pfxNemVc <- paste0(varPfxC, nemNamVc)
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213
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214 ## omnibus and post-hoc tests
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215
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216 nemMN <- t(apply(datMN, 2, function(varVn) {
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217
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218 pvaN <- kruskal.test(varVn ~ facFcVn)[["p.value"]]
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219 varNemMN <- posthoc.kruskal.nemenyi.test(varVn, facFcVn, "Tukey")[["p.value"]]
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220 c(pvaN, c(varNemMN))
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221
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222 }))
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223
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224 ## correction for multiple testing
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225
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226 nemMN <- apply(nemMN, 2,
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227 function(pvaVn) p.adjust(pvaVn, method = adjC))
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228 adjVn <- nemMN[, 1]
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229 sigVn <- as.numeric(adjVn < thrN)
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230 nemMN <- nemMN[, c(FALSE, nemVl)]
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231 colnames(nemMN) <- paste0(pfxNemVc, "_", adjC)
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232
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233 ## significance coding (0 = not significant, 1 = significant)
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234
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235 nemSigMN <- nemMN < thrN
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236 mode(nemSigMN) <- "numeric"
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237 colnames(nemSigMN) <- paste0(pfxNemVc, "_sig")
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238
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239 ## difference of the medians for each pairwise comparison
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240
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241 difMN <- sapply(1:nrow(nemClaMC), function(prwI) {
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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242 prwVc <- nemClaMC[prwI, ]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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243 prwVi <- which(facFcVn %in% prwVc)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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244 prwFacFc <- factor(as.character(facFcVn)[prwVi], levels = prwVc)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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245 apply(datMN[prwVi, ], 2, function(varVn) -diff(as.numeric(tapply(varVn, prwFacFc, function(x) median(x, na.rm = TRUE)))))
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246 })
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247 colnames(difMN) <- gsub("_sig", "_dif", colnames(nemSigMN))
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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248
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249 ## final aggregated table
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250
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251 resMN <- cbind(adjVn, sigVn, difMN, nemMN, nemSigMN)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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252 colnames(resMN)[1:2] <- paste0(varPfxC, c(adjC, "sig"))
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253
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254 varDF <- cbind.data.frame(varDF, as.data.frame(resMN))
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255
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256 ## graphic
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257
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258 pdf(pdfC, onefile = TRUE)
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259
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260 for(varI in 1:nrow(varDF)) {
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261
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262 if(sum(nemSigMN[varI, ]) > 0) {
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263
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264 varC <- rownames(varDF)[varI]
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265
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266 boxplot(datMN[, varI] ~ facFcVn,
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267 main = paste0(varC, " (", adjC, " = ", signif(adjVn[varI], 2), ")"))
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268
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269 for(nemI in 1:length(nemNamVc)) {
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270
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271 if(nemSigMN[varI, paste0(varPfxC, nemNamVc[nemI], "_sig")] == 1) {
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272
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273 nemClaVc <- nemClaMC[nemI, ]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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274 nemClaVl <- facFcVn %in% nemClaVc
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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275 nemFc <- facFcVn[nemClaVl, drop = TRUE]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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276 nemVc <- as.character(nemFc)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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277 names(nemVc) <- rownames(samDF)[nemClaVl]
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
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278 boxF(nemFc,
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279 datMN[nemClaVl, varI],
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280 paste0(varC, " (", adjC, " = ", signif(nemMN[varI, paste0(varPfxC, nemNamVc[nemI], "_", adjC)], 2), ")"),
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281 nemVc)
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283 }
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285 }
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287 }
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289 }
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291 dev.off()
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293 }
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295 names(sigVn) <- rownames(varDF)
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296 sigSumN <- sum(sigVn, na.rm = TRUE)
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297 if(sigSumN) {
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298 cat("\nThe following ", sigSumN, " variable", ifelse(sigSumN > 1, "s", ""), " (", round(sigSumN / length(sigVn) * 100), "%) ", ifelse(sigSumN > 1, "were", "was"), " found significant at the ", thrN, " level:\n", sep = "")
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299 cat(paste(rownames(varDF)[sigVn > 0], collapse = "\n"), "\n", sep = "")
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300 } else
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301 cat("\nNo significant variable found at the selected ", thrN, " level\n", sep = "")
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303 options(stingsAsFactors = strAsFacL)
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305 return(varDF)
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307 }
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310 boxF <- function(xFc,
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311 yVn,
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312 maiC,
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313 xVc) {
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315 boxLs <- boxplot(yVn ~ xFc,
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316 main = maiC)
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318 outVn <- boxLs[["out"]]
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320 if(length(outVn)) {
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321
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322 for(outI in 1:length(outVn)) {
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323 levI <- which(levels(xFc) == xVc[names(outVn)[outI]])
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324 text(levI,
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325 outVn[outI],
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326 labels = names(outVn)[outI],
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327 pos = ifelse(levI == 2, 2, 4))
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328 }
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329
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330 }
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331
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332 }