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1 #####################################################################################
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2 #Copyright (C) <2012>
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3 #
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4 #Permission is hereby granted, free of charge, to any person obtaining a copy of
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5 #this software and associated documentation files (the "Software"), to deal in the
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6 #Software without restriction, including without limitation the rights to use, copy,
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7 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
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8 #and to permit persons to whom the Software is furnished to do so, subject to
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9 #the following conditions:
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10 #
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11 #The above copyright notice and this permission notice shall be included in all copies
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12 #or substantial portions of the Software.
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13 #
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14 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
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15 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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16 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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17 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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18 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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19 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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20 #
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21 # This file is a component of the MaAsLin (Multivariate Associations Using Linear Models),
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22 # authored by the Huttenhower lab at the Harvard School of Public Health
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23 # (contact Timothy Tickle, ttickle@hsph.harvard.edu).
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24 #####################################################################################
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25
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26 inlinedocs <- function(
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27 ##author<< Curtis Huttenhower <chuttenh@hsph.harvard.edu> and Timothy Tickle <ttickle@hsph.harvard.edu>
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28 ##description<< Global project constants.
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29 ) { return( pArgs ) }
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30
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31 #General
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32 c_COMMA = ","
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33 c_DASH = "-"
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34
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35 #For reading IO
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36 c_MATRIX_NAME = "Matrix:"
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37 c_FILE_NAME = "File:"
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38 c_DELIMITER = "Delimiter:"
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39 c_ID_ROW = "Name_Row_Number:"
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40 c_ID_COLUMN = "Name_Column_Number:"
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41 c_ROWS = "Read_Rows:"
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42 c_PCLROWS = "Read_PCL_Rows:"
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43 c_TSVROWS = "Read_TSV_Rows:"
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44 c_COLUMNS = "Read_Columns:"
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45 c_PCLCOLUMNS = "Read_PCL_Columns:"
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46 c_TSVCOLUMNS = "Read_TSV_Columns:"
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47 c_CHARACTER_DATA_TYPE = "DT_Character:"
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48 c_FACTOR_DATA_TYPE = "DT_Factor:"
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49 c_INTEGER_DATA_TYPE = "DT_Integer:"
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50 c_LOGICAL_DATA_TYPE = "DT_Logical:"
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51 c_NUMERIC_DATA_TYPE = "DT_Numeric:"
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52 c_ORDEREDFACTOR_DATA_TYPE = "DT_Ordered_Factor:"
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53
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54 ### The name of the data matrix read in using a read.config file
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55 c_strMatrixData <- "Abundance"
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56 ### The name of the metadata matrix read in using a read.config file
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57 c_strMatrixMetadata <- "Metadata"
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58 # Settings for MFA visualization/ordination
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59 c_iMFA <- 30
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60 c_dHeight <- 9
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61 c_dDefaultScale = 0.5
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62 # The column that is used to determine if information meets a certain significance threshold (dSignificanceLevel) to include in the Summary text file)
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63 c_strKeywordEvaluatedForInclusion <- "Q.value"
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64 #The name of the custom process function
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65 c_strCustomProcessFunction = "processFunction"
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66
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67 #Delimiters
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68 #Feature name delimiter
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69 c_cFeatureDelim = "|"
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70 c_cFeatureDelimRex = "\\|"
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71
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72 #The word used for unclassified
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73 c_strUnclassified = "unclassified"
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74
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75 #Maaslincore settings
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76 #If a metadata does not have more than count of unique values, it is changed to factor data mode.
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77 c_iNonFactorLevelThreshold = 3
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78
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79 #Extensions
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80 c_sDetailFileSuffix = ".txt"
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81 c_sSummaryFileSuffix = ".txt"
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82 c_sLogFileSuffix = "_log"
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83
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84 #Delimiter for output tables
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85 c_cTableDelimiter="\t"
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86
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87 #Testing Related
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88 c_strTestingDirectory = "testing"
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89 c_strCorrectAnswers = "answers"
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90 c_strTemporaryFiles = "tmp"
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91 c_strTestingInput = "input"
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92
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93 #Reading matrix defaults
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94 c_strDefaultMatrixDelimiter = "\t"
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95 c_strDefaultMatrixRowID = "1"
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96 c_strDefaultMatrixColID = "1"
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97 c_strDefaultReadRows = "-"
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98 c_strDefaultReadCols = "-"
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99
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100 #Separator used when collapsing factor names
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101 c_sFactorNameSep = ""
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102
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103 #Separator used by the mfa
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104 c_sMFANameSep1 = "_"
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105 c_sMFANameSep2 = "."
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106
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107 #Analysis Module list positioning
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108 c_iSelection = 1
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109 c_iTransform = 2
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110 c_iAnalysis = 3
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111 c_iResults = 4
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112 c_iUnTransform = 5
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113 c_iIsUnivariate = 6
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114
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115 #Count based models
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116 c_vCountBasedModels = c("neg_binomial","quasi")
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117
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118 # Na action in anaylsis, placed here to standardize
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119 c_strNA_Action = "na.omit"
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