Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov_input.R @ 9:06c51af11531 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
author eschen42
date Fri, 10 Aug 2018 11:15:31 -0400
parents 066b1f409e9f
children 9a52306991b3
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1 # read_data_frame - read a w4m data frame, with error handling
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2 # e.g., data_matrix_input_env <- read_data_frame(dataMatrix_in, "data matrix input")
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3 read_data_frame <- function(file_path, kind_string, failure_action = failure_action) {
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4 my.env <- new.env()
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5 my.env$success <- FALSE
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6 my.env$msg <- sprintf("no message reading %s", kind_string)
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7 tryCatch(
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8 expr = {
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9 my.env$data <- utils::read.delim( fill = FALSE, file = file_path )
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10 my.env$success <- TRUE
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11 }
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12 , error = function(e) {
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13 my.env$ msg <- sprintf("%s read failed", kind_string)
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14 }
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15 )
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16 if (!my.env$success) {
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17 failure_action(my.env$msg)
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18 return ( FALSE )
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19 }
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20 return (my.env)
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21 }
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22
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23 # read one of three XCMS data elements: dataMatrix, sampleMetadata, variableMetadata
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24 # returns respectively: matrix, data.frame, data.frame, or FALSE if there is a failure
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25 read_xcms_data_element <- function(xcms_data_in, xcms_data_type, failure_action = stop) {
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26 # note that 'stop' effectively means 'throw'; if 'warning' and 'message' are caught, they mean 'throw' as well
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27 my_failure_action <- function(...) { failure_action("read_xcms_data_element: ", ...) }
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28 # xcms_data_type must be in c("sampleMetadata", "variableMetadata", "dataMatrix")
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29 if ( ! is.character(xcms_data_type) ) {
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30 my_failure_action(sprintf("bad parameter xcms_data_type '%s'", deparse(xcms_data_type)))
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31 return ( FALSE )
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32 }
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33 if ( 1 != length(xcms_data_type)
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34 || ! ( xcms_data_type %in% c("sampleMetadata", "variableMetadata", "dataMatrix") )
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35 ) {
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36 my_failure_action( sprintf("bad parameter xcms_data_type '%s'", xcms_data_type) )
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37 return ( FALSE )
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38 }
5
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39 if ( is.character(xcms_data_in) ) {
0
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40 # case: xcms_data_in is a path to a file
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41 xcms_data_input_env <- read_data_frame( xcms_data_in, sprintf("%s input", xcms_data_type) )
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42 if (!xcms_data_input_env$success) {
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43 my_failure_action(xcms_data_input_env$msg)
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44 return ( FALSE )
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45 }
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46 return ( xcms_data_input_env$data )
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47 } else {
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48 # case: xcms_data_in is invalid
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49 my_failure_action( sprintf("xcms_data_in has unexpected type %s", typeof(xcms_data_in)) )
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50 return ( FALSE )
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51 }
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52 }
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53
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54 read_inputs <- function(input_env, failure_action = print) {
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55 if ( ! is.environment(input_env) ) {
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56 failure_action("read_inputs: fatal error - 'input_env' is not an environment")
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57 return ( FALSE )
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58 }
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59
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60 if (!is.null(sampleMetadata_in <- input_env$sampleMetadata_in)) {
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61 # ---
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62 # read in the sample metadata
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63 read_data_result <- tryCatchFunc(
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64 expr = {
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65 read_xcms_data_element(xcms_data_in = sampleMetadata_in, xcms_data_type = "sampleMetadata")
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66 }
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67 )
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68 if ( read_data_result$success ) {
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69 smpl_metadata <- read_data_result$value
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70 } else {
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71 failure_action(read_data_result$msg)
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72 return ( FALSE )
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73 }
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74
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75 # extract rownames
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76 rownames(smpl_metadata) <- smpl_metadata[,1]
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77
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78 input_env$smpl_metadata <- smpl_metadata
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79 # ...
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80 } else {
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81 failure_action("read_inputs: fatal error - 'sampleMetadata_in' is missing from 'input_env'")
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82 return ( FALSE )
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83 }
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84
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85 if (!is.null(variableMetadata_in <- input_env$variableMetadata_in)) {
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diff changeset
86 # ---
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87 # read in the variable metadata
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88 read_data_result <- tryCatchFunc(
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89 expr = {
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90 read_xcms_data_element(xcms_data_in = variableMetadata_in, xcms_data_type = "variableMetadata")
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91 }
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92 )
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93 if ( read_data_result$success ) {
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94 vrbl_metadata <- read_data_result$value
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95 } else {
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96 failure_action(read_data_result$msg)
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97 return (FALSE)
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98 }
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99
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100
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101 # extract rownames (using make.names to handle degenerate feature names)
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102 err.env <- new.env()
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103 err.env$success <- FALSE
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104 err.env$msg <- "no message setting vrbl_metadata rownames"
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105 tryCatch(
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106 expr = {
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107 rownames(vrbl_metadata) <- make.names( vrbl_metadata[,1], unique = TRUE )
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108 vrbl_metadata[,1] <- rownames(vrbl_metadata)
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109 err.env$success <- TRUE
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110 }
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111 , error = function(e) {
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112 err.env$ msg <- sprintf("failed to set rownames for vrbl_metadata read because '%s'", e$message)
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113 }
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114 )
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115 if (!err.env$success) {
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116 failure_action(err.env$msg)
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117 return ( FALSE )
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118 }
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119
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120 input_env$vrbl_metadata <- vrbl_metadata
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121 # ...
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122 } else {
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123 failure_action("read_inputs: fatal error - 'variableMetadata_in' is missing from 'input_env'")
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124 return ( FALSE )
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125 }
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126
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127 if (!is.null(dataMatrix_in <- input_env$dataMatrix_in)) {
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128 # ---
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129 # read in the data matrix
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130 read_data_result <- tryCatchFunc(
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131 expr = {
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132 read_xcms_data_element(xcms_data_in = dataMatrix_in, xcms_data_type = "dataMatrix")
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133 }
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134 )
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135 if ( read_data_result$success ) {
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136 data_matrix <- read_data_result$value
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137 } else {
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138 failure_action(read_data_result$msg)
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139 return (FALSE)
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140 }
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141
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142 if ( ! is.matrix(data_matrix) ) {
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143 # extract rownames (using make.names to handle degenerate feature names)
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144 err.env <- new.env()
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145 err.env$success <- FALSE
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146 err.env$msg <- "no message setting data_matrix rownames"
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147 tryCatch(
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148 expr = {
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149 rownames(data_matrix) <- make.names( data_matrix[,1], unique = TRUE )
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150 err.env$success <- TRUE
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151 }
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152 , error = function(e) {
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153 err.env$msg <- sprintf("failed to set rownames for data_matrix read because '%s'", e$message)
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154 }
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155 )
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156 if (!err.env$success) {
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157 failure_action(err.env$msg)
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158 return ( FALSE )
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159 }
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160
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161 # remove rownames column
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162 data_matrix <- data_matrix[,2:ncol(data_matrix)]
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163
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164 # convert data_matrix to matrix from data.frame
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165 data_matrix <- as.matrix(data_matrix)
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166 }
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167
7
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168 # Omit any feature not found in variableMetadata and any sample not found in sampleMetadata
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169 # For something more elaborate, see https://github.com/HegemanLab/w4mclassfilter
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170 data_matrix <- data_matrix[rownames(data_matrix) %in% rownames(vrbl_metadata),colnames(data_matrix) %in% rownames(smpl_metadata)]
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171
0
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172 input_env$data_matrix <- data_matrix
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173 # ...
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174 } else {
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175 failure_action("read_inputs: fatal error - 'dataMatrix_in' is missing from 'input_env'")
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176 return ( FALSE )
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177 }
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178
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179 return ( TRUE )
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180 }
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181