Mercurial > repos > eschen42 > w4mclassfilter
comparison w4mclassfilter_wrapper.R @ 8:d5cf23369d12 draft
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
| author | eschen42 |
|---|---|
| date | Sat, 03 Mar 2018 22:58:14 -0500 |
| parents | 38ccf6722d54 |
| children | 38f509903a0b |
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| 7:582a8a42a93b | 8:d5cf23369d12 |
|---|---|
| 80 variableMetadata_in <- as.character(argVc["variableMetadata_in"]) | 80 variableMetadata_in <- as.character(argVc["variableMetadata_in"]) |
| 81 variableMetadata_out <- as.character(argVc["variableMetadata_out"]) | 81 variableMetadata_out <- as.character(argVc["variableMetadata_out"]) |
| 82 | 82 |
| 83 # other parameters | 83 # other parameters |
| 84 | 84 |
| 85 transformation <- as.character(argVc["transformation"]) | |
| 85 wildcards <- as.logical(argVc["wildcards"]) | 86 wildcards <- as.logical(argVc["wildcards"]) |
| 86 sampleclassNames <- as.character(argVc["sampleclassNames"]) | 87 sampleclassNames <- as.character(argVc["sampleclassNames"]) |
| 87 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] | 88 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] |
| 88 if (wildcards) { | 89 if (wildcards) { |
| 89 sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) | 90 sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) |
| 93 classnameColumn <- as.character(argVc["classnameColumn"]) | 94 classnameColumn <- as.character(argVc["classnameColumn"]) |
| 94 samplenameColumn <- as.character(argVc["samplenameColumn"]) | 95 samplenameColumn <- as.character(argVc["samplenameColumn"]) |
| 95 | 96 |
| 96 variable_range_filter <- as.character(argVc["variable_range_filter"]) | 97 variable_range_filter <- as.character(argVc["variable_range_filter"]) |
| 97 variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] | 98 variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]] |
| 99 | |
| 100 ## ----------------------------- | |
| 101 ## Transformation and imputation | |
| 102 ## ----------------------------- | |
| 103 my_w4m_filter_imputation <- if (transformation == "log10") { | |
| 104 function(m) { | |
| 105 if (!is.matrix(m)) | |
| 106 stop("Cannot impute and transform data - the supplied data is not in matrix form") | |
| 107 if (nrow(m) == 0) | |
| 108 stop("Cannot impute and transform data - data matrix has no rows") | |
| 109 if (ncol(m) == 0) | |
| 110 stop("Cannot impute and transform data - data matrix has no columns") | |
| 111 suppressWarnings( | |
| 112 # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step | |
| 113 m <- log10(m) | |
| 114 ) | |
| 115 return ( w4m_filter_imputation(m) ) | |
| 116 } | |
| 117 } else if (transformation == "log2") { | |
| 118 function(m) { | |
| 119 if (!is.matrix(m)) | |
| 120 stop("Cannot impute and transform data - the supplied data is not in matrix form") | |
| 121 if (nrow(m) == 0) | |
| 122 stop("Cannot impute and transform data - data matrix has no rows") | |
| 123 if (ncol(m) == 0) | |
| 124 stop("Cannot impute and transform data - data matrix has no columns") | |
| 125 suppressWarnings( | |
| 126 # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step | |
| 127 m <- log2(m) | |
| 128 ) | |
| 129 return ( w4m_filter_imputation(m) ) | |
| 130 } | |
| 131 } else { | |
| 132 # use the method from the w4mclassfilter class | |
| 133 w4m_filter_imputation | |
| 134 } | |
| 98 | 135 |
| 99 ##------------------------------ | 136 ##------------------------------ |
| 100 ## Computation | 137 ## Computation |
| 101 ##------------------------------ | 138 ##------------------------------ |
| 102 | 139 |
| 111 , include = inclusive | 148 , include = inclusive |
| 112 , class_column = classnameColumn | 149 , class_column = classnameColumn |
| 113 , samplename_column = samplenameColumn | 150 , samplename_column = samplenameColumn |
| 114 , variable_range_filter = variable_range_filter | 151 , variable_range_filter = variable_range_filter |
| 115 , failure_action = my_print | 152 , failure_action = my_print |
| 153 , data_imputation = my_w4m_filter_imputation | |
| 116 ) | 154 ) |
| 117 | 155 |
| 118 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", | 156 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", |
| 119 as.character(result), "\n", sep = "") | 157 as.character(result), "\n", sep = "") |
| 120 | 158 |