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comparison maaslin-4450aa4ecc84/src/test-Utility/test-Utility.R @ 1:a87d5a5f2776

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Uploaded the version running on the prod server
author george-weingart
date Sun, 08 Feb 2015 23:08:38 -0500
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0:e0b5980139d9 1:a87d5a5f2776
1 c_strDir <- file.path(getwd( ),"..")
2
3 source(file.path(c_strDir,"lib","Constants.R"))
4 source(file.path(c_strDir,"lib","Utility.R"))
5
6 context("Test funcRename")
7 test_that("Test that unclassified and none otus are represented as 2 terminal clades and others are 1",{
8 expect_equal(funcRename(paste("A","B","C","D",c_strUnclassified, sep=c_cFeatureDelim)),paste("D",c_strUnclassified, sep=c_cFeatureDelim))
9 expect_equal(funcRename(paste("A","B","C","D","101", sep=c_cFeatureDelim)),paste("D","101", sep=c_cFeatureDelim))
10 expect_equal(funcRename(paste("A","B","C","D", sep=c_cFeatureDelim)),paste("D", sep=c_cFeatureDelim))
11 expect_equal(funcRename(paste("A", sep=c_cFeatureDelim)),paste("A", sep=c_cFeatureDelim))
12 expect_equal(funcRename(paste(c_strUnclassified, sep=c_cFeatureDelim)),paste(c_strUnclassified, sep=c_cFeatureDelim))
13 expect_equal(funcRename(paste("101", sep=c_cFeatureDelim)),paste("101", sep=c_cFeatureDelim))
14 })
15
16 context("Test funcColorHelper")
17 test_that("Test that min is min and max is max and average is average even if given as NA",{
18 expect_equal(funcColorHelper( dMax = 1, dMin = 1, dMed = NA ), list( dMin = 1, dMax = 1, dMed = 1))
19 expect_equal(funcColorHelper( dMax = -3, dMin = 10, dMed = NA ), list( dMin = -3, dMax = 10, dMed = 3.5))
20 expect_equal(funcColorHelper( dMax = 1, dMin = 11, dMed = NA ), list( dMin = 1, dMax = 11, dMed = 6))
21 expect_equal(funcColorHelper( dMax = 4, dMin = 10, dMed = 5 ), list( dMin = 4, dMax = 10, dMed = 5))
22 expect_equal(funcColorHelper( dMax = 10, dMin = 4, dMed = 5 ), list( dMin = 4, dMax = 10, dMed = 5))
23 })
24
25 context("Test funcTrim")
26 test_that("Test that white spaces at the beginning and end of s string are removed",{
27 expect_equal(funcTrim("TRIM"),"TRIM")
28 expect_equal(funcTrim(" TRIM"),"TRIM")
29 expect_equal(funcTrim(" TRIM"),"TRIM")
30 expect_equal(funcTrim(" TRIM "),"TRIM")
31 expect_equal(funcTrim("TRIM "),"TRIM")
32 expect_equal(funcTrim(" TRIM "),"TRIM")
33 expect_equal(funcTrim("TR IM"),"TR IM")
34 expect_equal(funcTrim(" TR IM"),"TR IM")
35 expect_equal(funcTrim(" TR I M"),"TR I M")
36 expect_equal(funcTrim(" TR IM "),"TR IM")
37 expect_equal(funcTrim("T R IM "),"T R IM")
38 expect_equal(funcTrim(" T RIM "),"T RIM")
39 })
40
41 #TODO currently the capture versio of this does not produce a tabbed table (or default table delim) which is not consistent with the rest of the code base.
42 context("Test funcWrite")
43 #Answer files
44 c_sAnswerWriteFile1 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTemp1.txt")
45 c_sAnswerWriteFile2 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTemp2.txt")
46 print("c_sAnswerWriteFile2")
47 print(c_sAnswerWriteFile2)
48 c_sAnswerWriteDFFile1 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTempDF1.txt")
49 c_sAnswerWriteDFFile2 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTempDF2.txt")
50
51 #Working files
52 c_sTempWriteFile1 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTemp1.txt")
53 c_sTempWriteFile2 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTemp2.txt")
54 c_sTempWriteDFFile1 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTempDF1.txt")
55 c_sTempWriteDFFile2 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTempDF2.txt")
56 dfTest = as.data.frame(as.matrix(cbind(c(1,11,111),c(2,22,222),c(3,33,333))))
57 sWriteString = "Testing, 1,2,3 anything but that."
58 unlink(c_sTempWriteFile1)
59 unlink(c_sTempWriteFile2)
60 unlink(c_sTempWriteDFFile1)
61 unlink(c_sTempWriteDFFile2)
62 funcWrite(sWriteString,c_sTempWriteFile1)
63 funcWrite(sWriteString,c_sTempWriteFile2)
64 funcWrite(sWriteString,c_sTempWriteFile2)
65 funcWrite(dfTest,c_sTempWriteDFFile1)
66 funcWrite(dfTest,c_sTempWriteDFFile2)
67 funcWrite(dfTest,c_sTempWriteDFFile2)
68
69 test_that("Test that a test file is written and appended to for strings and dataframes.",{
70 expect_equal(readLines(c_sTempWriteFile1),readLines(c_sAnswerWriteFile1))
71 expect_equal(readLines(c_sTempWriteFile2),readLines(c_sAnswerWriteFile2))
72 expect_equal(readLines(c_sTempWriteDFFile1),readLines(c_sAnswerWriteDFFile1))
73 expect_equal(readLines(c_sTempWriteDFFile2),readLines(c_sAnswerWriteDFFile2))
74 })
75
76 context("Test funcWriteTable")
77 #Answer files
78 c_sAnswerWriteDFFile1 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTableTempDF1.txt")
79 c_sAnswerWriteDFFile2 = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncWriteTableTempDF2.txt")
80
81 #Working files
82 c_sTempWriteDFFile1 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTableTempDF1.txt")
83 c_sTempWriteDFFile2 = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncWriteTableTempDF2.txt")
84 unlink(c_sTempWriteDFFile1)
85 unlink(c_sTempWriteDFFile2)
86 funcWriteTable(dfTest,c_sTempWriteDFFile1)
87 funcWriteTable(dfTest,c_sTempWriteDFFile2, fAppend=TRUE)
88 funcWriteTable(dfTest,c_sTempWriteDFFile2, fAppend=TRUE)
89
90 test_that("Test that a test file is written and appended to for dataframes.",{
91 expect_equal(readLines(c_sTempWriteDFFile1),readLines(c_sAnswerWriteDFFile1))
92 expect_equal(readLines(c_sTempWriteDFFile2),readLines(c_sAnswerWriteDFFile2))
93 })
94
95 context("Test funcCoef2Col")
96 dfTestWithFactors = as.data.frame(as.matrix(cbind(c(1,11,111),c(2,22,222),c(3,33,333))))
97 colnames(dfTestWithFactors)=c("A","B","C")
98 dfTestWithFactors["B"]=as.factor(as.character(dfTestWithFactors[["B"]]))
99 test_that("Test that a coefficients are found or not given if they exist",{
100 expect_equal(funcCoef2Col(strCoef="C",frmeData=dfTestWithFactors,astrCols=c()),"C")
101 expect_equal(funcCoef2Col(strCoef="A",frmeData=dfTestWithFactors,astrCols=c()),"A")
102 expect_equal(funcCoef2Col(strCoef=paste("B","2",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
103 expect_equal(funcCoef2Col(strCoef=paste("B","22",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
104 expect_equal(funcCoef2Col(strCoef=paste("B","222",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
105 expect_equal(funcCoef2Col(strCoef="C",frmeData=dfTestWithFactors,astrCols=c("A","B","C")),"C")
106 expect_equal(funcCoef2Col(strCoef=paste("B","2",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("A","B")),"B")
107 expect_equal(funcCoef2Col(strCoef=paste("B","22",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("B","C")),"B")
108 expect_equal(funcCoef2Col(strCoef=paste("B","222",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("B")),"B")
109 })
110
111 context("Test funcMFAValue2Col")
112 dfTestWithFactors = data.frame(A=c(1,3,3,4,5,6,7,8),B=c(1.0,2.0, 5.8,4.6,4.7,8.9,9.0,2.0),C=c("one","two","one","two","one","two","one","two"),D=c("1","2","1","2","1","2","1","2"))
113 dfTestWithFactors["three"]=as.factor(dfTestWithFactors[["three"]])
114 test_that("Test that a column names is found or not given if they exist",{
115 expect_equal(funcMFAValue2Col(xValue=5.8,dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"B")
116 expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"A")
117 expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"C")
118 expect_equal(funcMFAValue2Col(xValue="two",dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"C")
119 expect_equal(funcMFAValue2Col(xValue=paste("D","1",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"D")
120 expect_equal(funcMFAValue2Col(xValue=paste("D","2",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"D")
121 expect_equal(funcMFAValue2Col(xValue=2.0,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,3)),NULL)
122 expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(2,3)),NULL)
123 expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,2)),NULL)
124 expect_equal(funcMFAValue2Col(xValue="two",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,2)),NULL)
125 expect_equal(funcMFAValue2Col(xValue=2.0,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(2)),"B")
126 expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1)),"A")
127 expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(3)),"C")
128 expect_equal(funcMFAValue2Col(xValue=paste("D","2",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(4)),"D")
129 })
130
131 context("Test funcFormulaStrToList")
132 test_that("List of covariates are given, from lm or mixed model formulas",{
133 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate`"),c("1Covariate"))
134 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate`"),c("1Covariate","2Covariate"))
135 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
136 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate`"),c("1Covariate"))
137 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate`"),c("1Covariate","2Covariate"))
138 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
139 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + `2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
140 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
141 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + 1|`2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
142 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
143 expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + `2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
144 expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + 1|`2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
145 })
146
147 context("Test funcFormulaListToString")
148 test_that("The correct string formula for a lm or mixed model is created from a list of covariates",{
149 expect_equal(funcFormulaListToString(NULL),c(NA,NA))
150 expect_equal(funcFormulaListToString(c("1Covariate")),c("adCur ~ `1Covariate`",NA))
151 expect_equal(funcFormulaListToString(c("1Covariate","2Covariate")),c("adCur ~ `1Covariate` + `2Covariate`",NA))
152 expect_equal(funcFormulaListToString(c("1Covariate","2Covariate","3Covariate")),c("adCur ~ `1Covariate` + `2Covariate` + `3Covariate`",NA))
153 expect_equal(funcFormulaListToString(c("1Covariate","2Covariate"),c("3Covariate")),c(NA,"adCur ~ `1Covariate` + `2Covariate` + 1|`3Covariate`"))
154 expect_equal(funcFormulaListToString(c("1Covariate","3Covariate"),c("2Covariate")),c(NA,"adCur ~ `1Covariate` + `3Covariate` + 1|`2Covariate`"))
155 expect_equal(funcFormulaListToString(c("2Covariate","3Covariate"),c("1Covariate")),c(NA,"adCur ~ `2Covariate` + `3Covariate` + 1|`1Covariate`"))
156 expect_equal(funcFormulaListToString(c("2Covariate"),c("1Covariate","3Covariate")),c(NA,"adCur ~ `2Covariate` + 1|`1Covariate` + 1|`3Covariate`"))
157 expect_equal(funcFormulaListToString(c("1Covariate"),c("2Covariate","3Covariate")),c(NA,"adCur ~ `1Covariate` + 1|`2Covariate` + 1|`3Covariate`"))
158 expect_equal(funcFormulaListToString(c("3Covariate"),c("1Covariate","2Covariate")),c(NA,"adCur ~ `3Covariate` + 1|`1Covariate` + 1|`2Covariate`"))
159 })