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annotate heatmap_script.R @ 0:ad06aeed02c9 draft

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planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
author ethevenot
date Tue, 02 Aug 2016 06:26:41 -0400
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ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
ethevenot
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1 ## Etienne Thevenot
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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2 ## CEA, MetaboHUB
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3 ## W4M Core Development Team
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4 ## etienne.thevenot@cea.fr
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5 ## 2015-05-30
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6
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7
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8 heatmapF <- function(proMN,
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9 obsDF,
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10 feaDF,
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11 disC, ## dissimilarity
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12 cutSamN, ## number of sample clusters
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13 cutVarN, ## number of variable clusters
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14 fig.pdfC,
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15 corMetC, ## correlation method
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16 aggMetC, ## agglomeration method
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17 colC, ## color scale
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18 scaL,
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19 cexN) {
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21 ncaN <- 14 ## Sample and variable name truncature for display
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22
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23 if(aggMetC == "ward") {
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25 rvsLs <- R.Version()
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26 aggMetC <- paste0(aggMetC,
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27 ifelse(as.numeric(rvsLs[["major"]]) > 3 ||
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28 as.numeric(rvsLs[["major"]]) == 3 && as.numeric(rvsLs[["minor"]]) > 0.3,
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29 ".D",
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30 ""))
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31
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32 }
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33
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34 if(disC %in% c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")) {
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35
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36 obsHcl <- hclust(dist(proMN, method = disC),
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37 method = aggMetC)
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38
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39 feaHcl <- hclust(dist(t(proMN), method = disC),
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40 method = aggMetC)
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41
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42 } else if(disC == "1-cor") {
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43
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44 obsHcl <- hclust(as.dist(1-cor(t(proMN),
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45 method = corMetC,
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46 use = "pairwise.complete.obs")),
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47 method = aggMetC)
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48
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49 feaHcl <- hclust(as.dist(1-cor(proMN,
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50 method = corMetC,
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51 use = "pairwise.complete.obs")),
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52 method = aggMetC)
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53
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54 } else if(disC == "1-abs(cor)") {
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55
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56 obsHcl <- hclust(as.dist(1-abs(cor(t(proMN),
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57 method = corMetC,
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58 use = "pairwise.complete.obs"))),
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59 method = aggMetC)
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60
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61 feaHcl <- hclust(as.dist(1-abs(cor(proMN,
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62 method = corMetC,
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63 use = "pairwise.complete.obs"))),
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64 method = aggMetC)
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65
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66 }
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67
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68 heaMN <- proMN <- proMN[obsHcl[["order"]], feaHcl[["order"]]]
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69
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70 if(scaL)
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71 heaMN <- scale(heaMN)
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72
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73 heaMN <- heaMN[, rev(1:ncol(heaMN)), drop = FALSE]
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74
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75 switch(colC,
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76 blueOrangeRed = {
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77 imaPalVn <- colorRampPalette(c("blue", "orange", "red"),
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78 space = "rgb")(5)[1:5]
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79 },
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80 redBlackGreen = {
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81 imaPalVn <- colorRampPalette(c("red", "black", "green"),
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82 space = "rgb")(5)[1:5]
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83 })
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84
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85
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86 ## figure
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87 ##-------
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88
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89 pdf(fig.pdfC,
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90 width = 14,
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91 height = 14)
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92
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93 layout(matrix(1:4, nrow = 2),
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94 widths = c(1, 9), heights = c(1, 9))
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diff changeset
95
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parents:
diff changeset
96 ## Color scale
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parents:
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97
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parents:
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98 scaN <- length(imaPalVn)
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ethevenot
parents:
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99
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100 par(mar = c(0.6, 0.6, 0.6, 4.1))
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101
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102 ylimVn <- c(0, scaN)
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103 ybottomVn <- 0:(scaN - 1)
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104 ytopVn <- 1:scaN
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105
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parents:
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106 plot(x = 0,
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107 y = 0,
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108 bty = "n",
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109 font.axis = 2,
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110 font.lab = 2,
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parents:
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111 type = "n",
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112 xlim = c(0, 1),
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parents:
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113 ylim = ylimVn,
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114 xlab = "",
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115 ylab = "",
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116 xaxs = "i",
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117 yaxs = "i",
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118 xaxt = "n",
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119 yaxt = "n")
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120
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121 rect(xleft = 0.8,
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122 ybottom = ybottomVn,
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123 xright = 1,
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124 ytop = ytopVn,
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125 col = imaPalVn,
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126 border = NA)
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127
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128 prtVn <- pretty(range(heaMN, na.rm = TRUE))
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129 axis(at = scaN / diff(range(prtVn)) * (prtVn - min(prtVn)),
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130 font = 2,
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131 font.axis = 2,
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132 labels = prtVn,
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133 las = 1,
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134 lwd = 2,
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135 lwd.ticks = 2,
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136 side = 4,
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137 xpd = TRUE)
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138
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139 arrows(par("usr")[2],
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140 par("usr")[4],
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141 par("usr")[2],
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diff changeset
142 par("usr")[3],
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143 code = 0,
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144 lwd = 2,
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145 xpd = TRUE)
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146
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147 ## Feature dendrogram
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148
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149 par(mar = c(7.1, 0.6, 0, 0.1),
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150 lwd = 2)
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151
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152 plot(rev(as.dendrogram(feaHcl)), horiz = TRUE,
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153 leaflab = "none",
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154 main = "", xaxs = "i", yaxs = "i",
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155 xaxt = "n", yaxt = "n", xlab = "", ylab = "")
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156
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157 revFeaHcl <- list(merge = cbind(feaHcl[["merge"]][, 2], feaHcl[["merge"]][, 1]),
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158 height = feaHcl[["height"]],
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159 order = rev(feaHcl[["order"]]),
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160 labels = feaHcl[["labels"]])
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161
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162 if(cutVarN > 1) {
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163 cluFeaVn <- cutree(revFeaHcl, k = cutVarN)[revFeaHcl[["order"]]]
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164 cutFeaVn <- which(abs(diff(cluFeaVn)) > 0)
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165 cutFeaTxtVn <- c(cutFeaVn[1] / 2, cutFeaVn + diff(c(cutFeaVn, length(cluFeaVn))) / 2) + 0.5
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166 cutFeaLinVn <- cutFeaVn + 0.5
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ethevenot
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167 text(par("usr")[1] + 0.2 * diff(par("usr")[1:2]),
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ethevenot
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168 cutFeaTxtVn,
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169 labels = unique(cluFeaVn),
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170 cex = 2,
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171 font = 2,
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172 las = 2)
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ethevenot
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173 }
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174
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175 ## Observation dendrogram
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176
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177 par(mar = c(0.1, 0, 0.6, 7.1),
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178 lwd = 2)
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179
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180 plot(as.dendrogram(obsHcl), leaflab = "none",
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181 main = "", xaxs = "i", yaxs = "i",
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182 yaxt = "n", xlab = "", ylab = "")
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183
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184 if(cutSamN > 1) {
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185 cluObsVn <- cutree(obsHcl, k = cutSamN)[obsHcl[["order"]]]
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186 cutObsVn <- which(abs(diff(cluObsVn)) > 0)
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187 cutObsTxtVn <- c(cutObsVn[1] / 2, cutObsVn + diff(c(cutObsVn, length(cluObsVn))) / 2) + 0.5
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188 cutObsLinVn <- cutObsVn + 0.5
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189 text(cutObsTxtVn,
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190 0.8 * par("usr")[4],
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191 labels = unique(cluObsVn),
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192 cex = 2,
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193 font = 2)
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194 }
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195
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196 ## Heatmap
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197
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198 par(mar = c(7.1, 0, 0, 7.1))
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199
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200 image(x = 1:nrow(heaMN),
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201 y = 1:ncol(heaMN),
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202 z = round(heaMN),
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203 col = imaPalVn,
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204 font.axis = 2,
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205 font.lab = 2,
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206 xaxt = "n",
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207 yaxt = "n",
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208 xlab = "",
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209 ylab = "")
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210
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211 obsOrdVc <- obsHcl[["labels"]][obsHcl[["order"]]]
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212 obsOrdLenVn <- sapply(obsOrdVc, nchar)
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213 obsOrdVc <- substr(obsOrdVc, 1, ncaN)
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214 obsOrdVc <- paste0(obsOrdVc, ifelse(obsOrdLenVn > ncaN, ".", ""), " ")
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215
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216 mtext(obsOrdVc,
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217 at = 1:nrow(heaMN),
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218 cex = cexN,
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219 las = 2,
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220 side = 1)
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221
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222 feaOrdVc <- feaHcl[["labels"]][feaHcl[["order"]]]
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223 feaOrdLenVn <- sapply(feaOrdVc, nchar)
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224 feaOrdVc <- substr(feaOrdVc, 1, ncaN)
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225 feaOrdVc <- paste0(" ", feaOrdVc, ifelse(feaOrdLenVn > ncaN, ".", ""))
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226
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227 mtext(feaOrdVc,
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228 at = ncol(heaMN):1,
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229 cex = cexN,
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230 las = 2,
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231 side = 4)
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232
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233 if(cutVarN > 1)
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234 abline(h = cutFeaLinVn)
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235 if(cutSamN > 1)
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236 abline(v = cutObsLinVn)
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237
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238 box()
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239
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240 dev.off()
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241
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242 ## Returning
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243 ##----------
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244
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245 if(cutSamN > 1)
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246 obsDF[, "heat_clust"] <- cutree(obsHcl, k = cutSamN)
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247 obsDF <- obsDF[obsHcl[["order"]], , drop = FALSE]
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248
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249 if(cutVarN > 1)
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250 feaDF[, "heat_clust"] <- cutree(feaHcl, k = cutVarN)
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251 feaDF <- feaDF[feaHcl[["order"]], , drop = FALSE]
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252
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253 return(invisible(list(proMN = proMN,
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254 obsDF = obsDF,
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255 feaDF = feaDF)))
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256
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257
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258 } ## end of heatmapF