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annotate w4m_general_purpose_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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6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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1 # prepare.data.matrix - Prepare x.datamatrix for multivariate statistical analaysis (MVA)
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2 # - Motivation:
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3 # - Selection:
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4 # - You may want to exclude several samples from your analysis:
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5 # - If so, set the argument 'exclude.samples' to a vector of sample names
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6 # - You may want to exclude several features or features from your analysis:
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7 # - If so, set the argument 'exclude.features' to a vector of feature names
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8 # - Renaming samples:
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9 # - You may want to rename several samples from your analysis:
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10 # - If so, set the argument 'sample.rename.function' to a function accepting a vector
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11 # of sample names and producing a vector of strings of equivalent length
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12 # - MVA is confounded by missing values.
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13 # - By default, this function imputes missing values as zero.
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14 # - For a different imputation, set the 'data.imputation' argument to a function
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15 # accepting a single matrix argument and returning a matrix of the same
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16 # dimensions as the argument.
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17 # - Transformation
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18 # - It may be desirable to transform the intensity data to reduce the range.
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19 # - By default, this function performs an eigth-root transformation:
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20 # - Any root-tranformation has the advantage of never being negative.
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21 # - Calculation of the eight-root is four times faster in my hands than log10.
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22 # - However, it has the disadvantage that calculation of fold-differences
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23 # is not additive as with log-transformation.
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24 # - Rather, you must divide the values and raise to the eighth power.
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25 # - For a different transformation, set the 'data.transformation' argument
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26 # to a function accepting a single matrix argument.
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27 # - The function should be written to return a matrix of the same dimensions
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28 # as the argument.
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29 # arguments:
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30 # - x.matrix - matrix of intensities (or data.frame of sample metadata)
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31 # - one row per sample
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32 # - one column per feature or metadata attribute
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33 # - exclude.samples - vector of labels of matrix rows (samples) to omit from analysis
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34 # - exclude.features - vector of labels of matrix columnss (features) to omit from analysis
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35 # - sample.rename.function - function to be used to rename rows if necessary, or NULL
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36 # - e.g., sample.rename.function = function(x) {
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37 # sub("(.*)_.*","\\1", row.names(x))
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38 # }
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39 # - data.imputation - function applied to matrix to impute missing values
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40 # - e.g., data.imputation = function(m) {
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41 # m[is.na(m)] <- min(m, na.rm = TRUE) / 100
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42 # return (m)
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43 # }
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44 # - data.transformation - function applied to matrix cells
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45 # - e.g., data.transformation = function(x) { return( log10(x) ) }
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46 # or, data.transformation = log10
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47 # result value:
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48 # transformed, imputed x.datamatrix with renamed rows and with neither excluded values nor features
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49 #
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50 ################################
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51 ##
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52 ## Notes regarding the effectiveness and performance of the data transformation method.
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53 ##
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54 ## The two transformations that I tried (log10 and 8th root) required different imputation methods.
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55 ##
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56 ## For the LCMS resin data set that I was working with, separation in MVA was nearly equivalent for:
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57 ## data.imputation <- function(x.matrix) {
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58 ## x.matrix[is.na(x.matrix)] <- 0
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59 ## return (x.matrix)
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60 ## }
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61 ## data.transformation <- function(x) {
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62 ## sqrt( sqrt( sqrt(x) ) )
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63 ## }
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64 ## and
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65 ## data.imputation <- function(x.matrix) {
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66 ## x.matrix[is.na(x.matrix)] <- min(x.matrix, na.rm = TRUE) / 100
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67 ## return (x.matrix)
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68 ## }
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69 ## data.transformation <- function(x) {
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70 ## log10(x)
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71 ## }
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72 ##
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73 ## Note further that triple application of the square root:
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74 ## - may be four times faster than log10:
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75 ## - may be three times faster than log2:
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76 ##
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77 ## system.time( junk <- sqrt( sqrt( sqrt(1:100000000) ) ) )
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78 ## user system elapsed
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79 ## 0.832 0.236 1.069
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80 ## system.time( junk <- log10(1:100000000) )
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81 ## user system elapsed
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82 ## 3.936 0.400 4.337
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83 ## system.time( junk <- log2(1:100000000) )
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84 ## user system elapsed
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85 ## 2.784 0.320 3.101
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
86 ##
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
87 ################################
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
88 #
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
89 prepare.data.matrix <- function(
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
90 x.matrix
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
91 , exclude.samples = NULL
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
92 , exclude.features = NULL
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
93 , sample.rename.function = NULL
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
94 , data.imputation =
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
95 function(m) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
96 # replace NA values with zero
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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97 m[is.na(m)] <- 0
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
98 # replace negative values with zero, if applicable (It should never be applicable!)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
99 if (min(m < 0)) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
100 m <- matrix(lapply(X = m, FUN = function(z) {max(z,0)}), nrow = nrow(m) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
101 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
102 # return matrix as the result
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
103 return (m)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
104 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
105 , data.transformation = function(x) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
106 sqrt( sqrt( sqrt(x) ) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
107 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
108 , en = new.env()
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
109 ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
110 # MatVar - Compute variance of rows or columns of a matrix
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
111 # ref: http://stackoverflow.com/a/25100036
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
112 # For row variance, dim == 1, for col variance, dim == 2
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
113 MatVar <- function(x, dim = 1) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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114 if (dim == 1) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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115 dim.x.2 <- dim(x)[2]
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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116 if ( dim.x.2 == 0 )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
117 stop("MatVar: there are zero columns")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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118 if ( dim.x.2 == 1 ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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119 stop("MatVar: a single column is insufficient to calculate a variance")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
120 # return ( rep.int(x = 0, times = nrow(x)) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
121 } else {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
122 return ( rowSums( (x - rowMeans(x))^2 ) / ( dim(x)[2] - 1 ) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
123 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
124 } else if (dim == 2) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
125 dim.x.1 <- dim(x)[1]
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
126 if ( dim.x.1 == 0 ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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127 stop("MatVar: there are zero rows")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
128 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
129 if ( dim.x.1 == 1 ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
130 stop("MatVar: a single row is insufficient to calculate a variance")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
131 # return ( rep.int(x = 0, times = ncol(x)) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
132 } else {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
133 return ( rowSums( (t(x) - colMeans(x))^2 ) / ( dim(x)[1] - 1 ) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
134 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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135 } else stop("Please enter valid dimension, for rows, dim = 1; for colums, dim = 2")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
136 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
137
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
138 nonzero.var <- function(x) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
139 if (nrow(x) == 0) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
140 print(str(x))
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
141 stop("matrix has no rows")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
142 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
143 if (ncol(x) == 0) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
144 print(str(x))
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
145 stop("matrix has no columns")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
146 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
147 if ( is.numeric(x) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
148 # exclude any rows with zero variance
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
149 row.vars <- MatVar(x, dim = 1)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
150 nonzero.row.vars <- row.vars > 0
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
151 nonzero.rows <- row.vars[nonzero.row.vars]
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
152 if ( length(rownames(x)) != length(rownames(nonzero.rows)) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
153 row.names <- attr(nonzero.rows,"names")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
154 x <- x[ row.names, , drop = FALSE ]
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
155 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
156
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
157 # exclude any columns with zero variance
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
158 column.vars <- MatVar(x, dim = 2)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
159 nonzero.column.vars <- column.vars > 0
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
160 nonzero.columns <- column.vars[nonzero.column.vars]
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
161 if ( length(colnames(x)) != length(colnames(nonzero.columns)) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
162 column.names <- attr(nonzero.columns,"names")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
163 x <- x[ , column.names, drop = FALSE ]
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
164 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
165 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
166 return (x)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
167 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
168
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
169 if (is.null(x.matrix)) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
170 stop("FATAL ERROR - prepare.data.matrix was called with null x.matrix")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
171 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
172
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
173 en$xpre <- x <- x.matrix
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
174
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
175 # exclude any samples as indicated
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176 if ( !is.null(exclude.features) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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177 my.colnames <- colnames(x)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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178 my.col.diff <- setdiff(my.colnames, exclude.features)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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179 x <- x[ , my.col.diff , drop = FALSE ]
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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180 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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181
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
182 # exclude any features as indicated
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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183 if ( !is.null(exclude.samples) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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184 my.rownames <- rownames(x)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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185 my.row.diff <- setdiff(my.rownames, exclude.samples)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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186 x <- x[ my.row.diff, , drop = FALSE ]
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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187 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
188
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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189 # rename rows if desired
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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190 if ( !is.null(sample.rename.function) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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191 renamed <- sample.rename.function(x)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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192 rownames(x) <- renamed
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193 }
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diff changeset
194
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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195 # save redacted x.datamatrix to environment
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196 en$redacted.data.matrix <- x
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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197
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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198 # impute values missing from the x.datamatrix
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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199 if ( !is.null(data.imputation) ) {
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200 x <- data.imputation(x)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
201 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
202
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
203 # perform transformation if desired
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204 if ( !is.null(data.transformation) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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205 x <- data.transformation(x)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
206 } else {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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207 x <- x
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
208 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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209
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
210 # purge rows and columns that have zero variance
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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211 if ( is.numeric(x) ) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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212 x <- nonzero.var(x)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
213 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
214
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
215 # save imputed, transformed x.datamatrix to environment
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
216 en$imputed.transformed.data.matrix <- x
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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217
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
218 return(x)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
219 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
220
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
221
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
222 ##-----------------------------------------------
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
223 ## helper functions for error detection/reporting
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diff changeset
224 ##-----------------------------------------------
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
225
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
226 # log-printing to stderr
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diff changeset
227 log_print <- function(x, ...) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
228 cat(
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
229 format(Sys.time(), "%Y-%m-%dT%H:%M:%S%z")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
230 , " "
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
231 , c(x, ...)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
232 , "\n"
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
233 , sep=""
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
234 , file=stderr()
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
235 )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
236 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
237
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
238 # tryCatchFunc produces a list
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
239 # On success of expr(), tryCatchFunc produces
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
240 # list(success TRUE, value = expr(), msg = "")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
241 # On failure of expr(), tryCatchFunc produces
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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242 # list(success = FALSE, value = NA, msg = "the error message")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
243 tryCatchFunc <- function(expr) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
244 # format error for logging
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
245 format_error <- function(e) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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246 paste(c("Error { message:", e$message, ", call:", e$call, "}"), collapse = " ")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
247 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
248 my_expr <- expr
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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249 retval <- NULL
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diff changeset
250 tryCatch(
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
251 expr = {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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252 retval <- ( list( success = TRUE, value = my_expr(), msg = "" ) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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253 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
254 , error = function(e) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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255 retval <<- list( success = FALSE, value = NA, msg = format_error(e) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
256 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
257 )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
258 return (retval)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
259 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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260
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
diff changeset
261 # tryCatchProc produces a list
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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diff changeset
262 # On success of expr(), tryCatchProc produces
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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263 # list(success TRUE, msg = "")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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264 # On failure of expr(), tryCatchProc produces
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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265 # list(success = FALSE, msg = "the error message")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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266 tryCatchProc <- function(expr) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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267 # format error for logging
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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268 format_error <- function(e) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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269 paste(c("Error { message:", e$message, ", call:", e$call, "}"), collapse = " ")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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270 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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271 retval <- NULL
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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272 tryCatch(
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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273 expr = {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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274 expr()
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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275 retval <- ( list( success = TRUE, msg = "" ) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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276 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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277 , error = function(e) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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278 retval <<- list( success = FALSE, msg = format_error(e) )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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279 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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280 )
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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281 return (retval)
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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282 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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283