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annotate w4mkmeans_routines.R @ 0:6ccbe18131a6 draft

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planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
author eschen42
date Tue, 08 Aug 2017 15:30:38 -0400
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children 02cafb660b72
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6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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1 ##------------------------------------------------------------------------------------------------------
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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2 ## these are the batch-independent and file-structure-independent routines to support the w4mkmeans tool
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3 ##------------------------------------------------------------------------------------------------------
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4
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5 library(parallel)
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6
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7 w4kmeans_usage <- function() {
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8 return (
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9 c(
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10 "w4mkmeans: bad input.",
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11 "# contract:",
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12 " required - caller will provide an environment comprising:",
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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13 " log_print - a logging function with the signature function(x, ...) expecting strings as x and ...",
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14 " variableMetadata - the corresponding W4M data.frame having feature metadata",
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15 " sampleMetdata - the corresponding W4M data.frame having sample metadata",
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16 " dataMatrix - the corresponding W4M matrix",
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17 " slots - the number of parallel slots for calculating kmeans",
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18 " optional - environment may comprise:",
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19 " kfeatures - an array of integers, the k's to apply for clustering by feature (default, empty array)",
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20 " ksamples - an array of integers, the k's to apply for clustering by sample (default, empty array)",
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21 " iter.max - the maximum number of iterations when calculating a cluster (default = 10)",
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22 " nstart - how many random sets of centers should be chosen (default = 1)",
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23 " algorithm - string from c('Hartigan-Wong', 'Lloyd', 'Forgy', 'MacQueen') (default = Hartigan-Wong)",
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24 " ",
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25 " this routine will return a list comprising:",
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26 " variableMetadata - the input variableMetadata data.frame with updates, if any",
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27 " sampleMetadata - the input sampleMetadata data.frame with updates, if any",
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28 " scores - an array of strings, each representing a line of a tsv having the following header:",
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29 " clusterOn TAB k TAB totalSS TAB betweenSS TAB proportion"
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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 w4mkmeans <- function(env) {
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35 # abort if 'env' is null or is not an environment
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36 if ( is.null(env) || ! is.environment(env) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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37 lapply(w4kmeans_usage(),print)
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38 }
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39 # supply default arguments
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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40 if ( ! exists("iter.max" , env) ) env$iter.max <- 10
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41 if ( ! exists("nstart" , env) ) env$nstart <- 1
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42 if ( ! exists("algorithm", env) ) env$algorithm <- 'Hartigan-Wong'
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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43 if ( ! exists("ksamples" , env) ) env$ksamples <- c()
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44 if ( ! exists("kfeatures", env) ) env$kfeatures <- c()
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45 # check mandatory arguments
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46 expected <- c(
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47 "log_print"
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48 , "variableMetadata"
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49 , "sampleMetadata"
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50 , "dataMatrix"
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51 , "slots"
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52 )
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53 missing_from_env <- setdiff(expected, (ls(env)))
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54 if ( length(missing_from_env) > 0 ) {
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55 print(paste(c('expected environment members not found: ', as.character(missing_from_env)), collapse = ", "))
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56 lapply(w4kmeans_usage(),print)
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57 stop("w4mkmeans: contract has been broken")
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58 }
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59 # extract parameters from 'env'
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60 failure_action <- env$log_print
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61 scores <- c( "clusterOn\tk\ttotalSS\tbetweenSS\tproportion" )
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62 sampleMetadata <- env$sampleMetadata
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63 featureMetadata <- env$variableMetadata
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64 ksamples <- as.numeric(env$ksamples)
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65 kfeatures <- as.numeric(env$kfeatures)
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66 slots <- env$slots
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67
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68 myLapply <- parLapply
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69 # uncomment the next line to mimic parLapply, but without parallelization (for testing/experimentation)
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70 # myLapply <- function(cl, ...) lapply(...)
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71 cl <- NULL
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72 if ( identical(myLapply, parLapply) ) {
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73 failure_action(sprintf("w4mkmeans: using parallel evaluation with %d slots", slots))
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74 failure_action(names(cl))
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75 cl <- makePSOCKcluster(names = slots)
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76 # from ?makePSOCKcluster: "It is good practice to shut down the workers by calling stopCluster."
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77 clusterExport(
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78 cl = cl
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79 , varlist = c(
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80 "tryCatchFunc"
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81 , "calc_kmeans_one_dimension_one_k"
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82 , "prepare.data.matrix"
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83 )
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84 )
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85 final <- function(cl) {
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86 # from ?makePSOCKcluster: "It is good practice to shut down the workers by calling stopCluster."
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87 if ( !is.null(cl) ) {
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88 failure_action("w4mkmeans: stopping cluster used for parallel evaluation")
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89 stopCluster(cl)
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90 }
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91 }
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92 } else {
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93 failure_action("w4mkmeans: using sequential evaluation (1 slot)")
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94 final <- function(cl) { }
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95 }
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96
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97 tryCatch(
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98 expr = {
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99 # These myLapply calls produce lists of lists of results:
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100 # - The outer list has no keys and its members are accessed by index
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101 # - The inner list has keys "clusters" and "scores"
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102
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103 # for each $i in ksamples, append column 'k$i' to data frame sampleMetadata
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104 ksamples_length <- length(ksamples)
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105 if ( ksamples_length > 0 ) {
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106 smpl_result_list <- myLapply(
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107 cl = cl
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108 , ksamples
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109 , calc_kmeans_one_dimension_one_k
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110 , env = env
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111 , dimension = "samples"
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112 )
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113 for ( i in 1:ksamples_length ) {
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114 result <- smpl_result_list[[i]]
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115 if (result$success) {
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116 sampleMetadata[sprintf("k%d",ksamples[i])] <- result$value$clusters
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117 scores <- c(scores, result$value$scores)
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118 }
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119 }
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120 }
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121
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122 # for each $i in kfeatures, append column 'k$i' to data frame featureMetadata
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123 kfeatures_length <- length(kfeatures)
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124 if ( kfeatures_length > 0 ) {
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125 feat_result_list <- myLapply(
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126 cl = cl
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127 , kfeatures
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128 , calc_kmeans_one_dimension_one_k
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129 , env = env
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130 , dimension = "features"
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131 )
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132 for ( i in 1:kfeatures_length ) {
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133 result <- feat_result_list[[i]]
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134 if (result$success) {
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135 featureMetadata[sprintf("k%d",kfeatures[i])] <- result$value$clusters
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136 scores <- c(scores, result$value$scores)
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137 }
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138 }
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139 }
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140
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141 return (
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142 list(
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143 variableMetadata = featureMetadata
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144 , sampleMetadata = sampleMetadata
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145 , scores = scores
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146 )
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147 )
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148 }
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149 , finally = final(cl)
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150 )
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151 }
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152
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153 # calculate k-means for features or samples
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154 # - recall that the dataMatrix has features in rows and samples in columns
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155 # return value:
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156 # list(clusters = km$cluster, scores = scores)
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157 # arguments:
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158 # env:
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159 # environment having dataMatrix
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160 # dimension:
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161 # - "samples": produce clusters column to add to the sampleMetadata table
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162 # - this is the default case
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163 # - "variables": produce clusters column to add to the variableMetadata table
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164 # k:
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165 # integer, the number of clusters to make
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166 calc_kmeans_one_dimension_one_k <- function(k, env, dimension = "samples") {
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167 # abort if environment is not as expected
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168 if ( is.null(env) || ! is.environment(env) ) {
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169 stop("calc_kmeans_one_dimension_one_k - argument 'env' is not an environment")
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170 }
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171 if ( ! exists("log_print", env) || ! is.function(env$log_print) ) {
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172 stop("calc_kmeans_one_dimension_one_k - argument 'env' - environment does not include log_print or it is not a function")
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173 }
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174 # abort if k is not as expected
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175 if ( ! is.numeric(k) ) {
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176 stop(sprintf("calc_kmeans_one_dimension_one_k - expected numeric argument 'k' but type is %s", typeof(k)))
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177 }
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178 k <- as.integer(k)
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179 # abort if dimension is not as expected
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180 if ( ! is.character(dimension)
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181 || ! Reduce( f =`|`, x = sapply(X = c("features","samples"), FUN = `==`, dimension), init = FALSE) ) {
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182 stop("calc_kmeans_one_dimension_one_k - argument 'dimension' is neither 'features' nor 'samples'")
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183 }
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184 dm <- env$dataMatrix
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185 iter.max <- env$iter.max
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186 nstart <- env$nstart
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187 algorithm <- env$algorithm
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188 dim_features <- dimension == "features"
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189 # tryCatchFunc produces a list
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190 # On success of expr(), tryCatchFunc produces
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191 # list(success TRUE, value = expr(), msg = "")
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192 # On failure of expr(), tryCatchFunc produces
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193 # list(success = FALSE, value = NA, msg = "the error message")
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194 result_list <- tryCatchFunc( expr = function() {
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195 # kmeans clusters the rows; features are the columns of args_env$dataMatrix; samples, the rows
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196 # - to calculate sample-clusters, no transposition is needed because samples are rows
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197 # - to calculate feature-clusters, transposition is needed so that features will be the rows
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198 if ( ! dim_features ) dm <- t(dm)
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199 dm <- prepare.data.matrix( x.matrix = dm, data.transformation = function(x) { x } )
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200 # need to set.seed to get reproducible results from kmeans
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201 set.seed(4567)
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202 # do the k-means clustering
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203 km <- kmeans( x = dm, centers = k, iter.max, nstart = nstart, algorithm = algorithm )
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204 scores <-
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205 sprintf("%s\t%d\t%0.5e\t%0.5e\t%0.5f"
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206 , dimension
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207 , k
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208 , km$totss
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209 , km$betweenss
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210 , km$betweenss/km$totss
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211 )
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212 list(clusters = km$cluster, scores = scores)
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213 })
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214 return ( result_list )
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215 }
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216