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Updated the structure of the libraries
author george.weingart@gmail.com
date Mon, 09 Feb 2015 12:17:40 -0500
parents e0b5980139d9
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7:c72e14eabb08 8:e9677425c6c3
1 #####################################################################################
2 #Copyright (C) <2012>
3 #
4 #Permission is hereby granted, free of charge, to any person obtaining a copy of
5 #this software and associated documentation files (the "Software"), to deal in the
6 #Software without restriction, including without limitation the rights to use, copy,
7 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
8 #and to permit persons to whom the Software is furnished to do so, subject to
9 #the following conditions:
10 #
11 #The above copyright notice and this permission notice shall be included in all copies
12 #or substantial portions of the Software.
13 #
14 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
15 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
16 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
17 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
18 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
19 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
20 #
21 # This file is a component of the MaAsLin (Multivariate Associations Using Linear Models),
22 # authored by the Huttenhower lab at the Harvard School of Public Health
23 # (contact Timothy Tickle, ttickle@hsph.harvard.edu).
24 #####################################################################################
25
26 inlinedocs <- function(
27 ##author<< Curtis Huttenhower <chuttenh@hsph.harvard.edu> and Timothy Tickle <ttickle@hsph.harvard.edu>
28 ##description<< Global project constants.
29 ) { return( pArgs ) }
30
31 #General
32 c_COMMA = ","
33 c_DASH = "-"
34
35 #For reading IO
36 c_MATRIX_NAME = "Matrix:"
37 c_FILE_NAME = "File:"
38 c_DELIMITER = "Delimiter:"
39 c_ID_ROW = "Name_Row_Number:"
40 c_ID_COLUMN = "Name_Column_Number:"
41 c_ROWS = "Read_Rows:"
42 c_PCLROWS = "Read_PCL_Rows:"
43 c_TSVROWS = "Read_TSV_Rows:"
44 c_COLUMNS = "Read_Columns:"
45 c_PCLCOLUMNS = "Read_PCL_Columns:"
46 c_TSVCOLUMNS = "Read_TSV_Columns:"
47 c_CHARACTER_DATA_TYPE = "DT_Character:"
48 c_FACTOR_DATA_TYPE = "DT_Factor:"
49 c_INTEGER_DATA_TYPE = "DT_Integer:"
50 c_LOGICAL_DATA_TYPE = "DT_Logical:"
51 c_NUMERIC_DATA_TYPE = "DT_Numeric:"
52 c_ORDEREDFACTOR_DATA_TYPE = "DT_Ordered_Factor:"
53
54 ### The name of the data matrix read in using a read.config file
55 c_strMatrixData <- "Abundance"
56 ### The name of the metadata matrix read in using a read.config file
57 c_strMatrixMetadata <- "Metadata"
58 # Settings for MFA visualization/ordination
59 c_iMFA <- 30
60 c_dHeight <- 9
61 c_dDefaultScale = 0.5
62 # The column that is used to determine if information meets a certain significance threshold (dSignificanceLevel) to include in the Summary text file)
63 c_strKeywordEvaluatedForInclusion <- "Q.value"
64 #The name of the custom process function
65 c_strCustomProcessFunction = "processFunction"
66
67 #Delimiters
68 #Feature name delimiter
69 c_cFeatureDelim = "|"
70 c_cFeatureDelimRex = "\\|"
71
72 #The word used for unclassified
73 c_strUnclassified = "unclassified"
74
75 #Maaslincore settings
76 #If a metadata does not have more than count of unique values, it is changed to factor data mode.
77 c_iNonFactorLevelThreshold = 3
78
79 #Extensions
80 c_sDetailFileSuffix = ".txt"
81 c_sSummaryFileSuffix = ".txt"
82 c_sLogFileSuffix = "_log"
83
84 #Delimiter for output tables
85 c_cTableDelimiter="\t"
86
87 #Testing Related
88 c_strTestingDirectory = "testing"
89 c_strCorrectAnswers = "answers"
90 c_strTemporaryFiles = "tmp"
91 c_strTestingInput = "input"
92
93 #Reading matrix defaults
94 c_strDefaultMatrixDelimiter = "\t"
95 c_strDefaultMatrixRowID = "1"
96 c_strDefaultMatrixColID = "1"
97 c_strDefaultReadRows = "-"
98 c_strDefaultReadCols = "-"
99
100 #Separator used when collapsing factor names
101 c_sFactorNameSep = ""
102
103 #Separator used by the mfa
104 c_sMFANameSep1 = "_"
105 c_sMFANameSep2 = "."
106
107 #Analysis Module list positioning
108 c_iSelection = 1
109 c_iTransform = 2
110 c_iAnalysis = 3
111 c_iResults = 4
112 c_iUnTransform = 5
113 c_iIsUnivariate = 6
114
115 #Count based models
116 c_vCountBasedModels = c("neg_binomial","quasi")
117
118 # Na action in anaylsis, placed here to standardize
119 c_strNA_Action = "na.omit"