Mercurial > repos > earlhaminst > plotheatmap

annotate script.R @ 1:05fbc5c891c5 draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
author earlhaminst
date Mon, 24 Feb 2025 11:03:02 +0000
parents bd8fd161908b
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bd8fd161908b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap commit 7e9d6b283879b45d5fe673767668c06104d31609-dirty
earlhaminst
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1 #!/usr/bin/env Rscript
bd8fd161908b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap commit 7e9d6b283879b45d5fe673767668c06104d31609-dirty
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earlhaminst
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3 args <- commandArgs(TRUE)
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
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4 countDataPath <- args[1]
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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5 statsDataPath <- args[2]
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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6 logFC <- args[3]
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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7 logCPM <- args[4]
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8 pValue <- args[5]
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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9 fdr <- args[6]
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11 clusterRow <- args[7]
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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12 clusterCol <- args[8]
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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13 hclustMethod <- args[9]
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15 mgColumnNm <- as.numeric(args[10])
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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16 mgRowNm <- as.numeric(args[11])
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18 pdfWidth <- as.numeric(args[12])
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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19 pdfHeight <- as.numeric(args[13])
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22 if (clusterRow == "Yes") {
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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23 clusterRow <- TRUE
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24 } else {
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25 clusterRow <- NA
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26 }
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28 if (clusterCol == "Yes") {
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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29 clusterCol <- TRUE
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30 } else {
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31 clusterCol <- NA
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32 }
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34 require(preprocessCore)
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35 require(gplots)
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37 # prepare counts data --------------------------------------------------------
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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38 countData <- read.table(countDataPath,
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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39 comment = "",
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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40 sep = "\t"
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41 )
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43 groups <- sapply(as.character(countData[1, -1]), strsplit, ":")
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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44 groups <- as.vector(t(countData[1, -1]))
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46 names <- as.vector(t(countData[2, -1]))
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48 countData <- countData[-c(1, 2), ]
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49 rownames(countData) <- countData[, 1]
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50 countData <- countData[, -1]
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51 colnames(countData) <- names
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53 countData <- countData[, order(groups, names)]
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55 # prepare stats data ------------------------------------------------------
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57 statsData <- read.table(statsDataPath,
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58 sep = "\t",
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59 header = T
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60 )
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62 colnames(statsData)[-1] <- sapply(colnames(statsData)[-1], function(x) {
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63 unlist(strsplit(x, ".", fixed = T))[3]
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64 })
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66 wh <- which(abs(statsData$logFC) >= logFC & statsData$logCPM >= logCPM & statsData$PValue <= pValue & statsData$FDR <= fdr)
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68 for (i in 1:ncol(countData)) {
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69 countData[, i] <- as.numeric(countData[, i])
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70 }
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72 countDataNorm <- normalize.quantiles(as.matrix(countData), copy = T)
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73 countDataNormLog <- log(countDataNorm + 1, 2)
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75 colnames(countDataNormLog) <- colnames(countData)
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76 rownames(countDataNormLog) <- rownames(countData)
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78 # svg("heatmap.svg", width = 3+length(names), height = 1/2*length(wh))
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79 pdf("heatmap.pdf", width = pdfWidth, height = pdfHeight)
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81 heatmap.2(
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82 countDataNormLog[wh, ],
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83 density.info = c("none"),
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84 hclustfun = function(x) hclust(x, method = hclustMethod),
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85 distfun = function(x) as.dist(1 - cor(t(x))),
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86 col = bluered(50),
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87 scale = "row",
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88 trace = "none",
05fbc5c891c5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
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89 Rowv = clusterRow,
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90 Colv = clusterCol,
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91 margins = c(mgColumnNm, mgRowNm)
0
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92 )
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93
bd8fd161908b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap commit 7e9d6b283879b45d5fe673767668c06104d31609-dirty
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94 dev.off()