maaslin: Maaslin

c_strCWD <- getwd()
c_strDir <- file.path(getwd( ),"..","..")

source(file.path(c_strDir,"R","lib","Constants.R"))
source(file.path(c_strDir,"R","lib","Utility.R"))

context("Test funcRename")
test_that("Test that unclassified and none otus are represented as 2 terminal clades and others are 1",{
  expect_equal(funcRename(paste("A","B","C","D",c_strUnclassified, sep=c_cFeatureDelim)),paste("D",c_strUnclassified, sep=c_cFeatureDelim))
  expect_equal(funcRename(paste("A","B","C","D","101", sep=c_cFeatureDelim)),paste("D","101", sep=c_cFeatureDelim))
  expect_equal(funcRename(paste("A","B","C","D", sep=c_cFeatureDelim)),paste("D", sep=c_cFeatureDelim))
  expect_equal(funcRename(paste("A", sep=c_cFeatureDelim)),paste("A", sep=c_cFeatureDelim))
  expect_equal(funcRename(paste(c_strUnclassified, sep=c_cFeatureDelim)),paste(c_strUnclassified, sep=c_cFeatureDelim))
  expect_equal(funcRename(paste("101", sep=c_cFeatureDelim)),paste("101", sep=c_cFeatureDelim))
})

context("Test funcColorHelper")
test_that("Test that min is min and max is max and average is average even if given as NA",{
  expect_equal(funcColorHelper( dMax = 1, dMin = 1, dMed = NA ), list( dMin = 1, dMax = 1, dMed = 1))
  expect_equal(funcColorHelper( dMax = -3, dMin = 10, dMed = NA ), list( dMin = -3, dMax = 10, dMed = 3.5))
  expect_equal(funcColorHelper( dMax = 1, dMin = 11, dMed = NA ), list( dMin = 1, dMax = 11, dMed = 6))
  expect_equal(funcColorHelper( dMax = 4, dMin = 10, dMed = 5 ), list( dMin = 4, dMax = 10, dMed = 5))
  expect_equal(funcColorHelper( dMax = 10, dMin = 4, dMed = 5 ), list( dMin = 4, dMax = 10, dMed = 5))
})

context("Test funcTrim")
test_that("Test that white spaces at the beginning and end of s string are removed",{
  expect_equal(funcTrim("TRIM"),"TRIM")
  expect_equal(funcTrim(" TRIM"),"TRIM")
  expect_equal(funcTrim("  TRIM"),"TRIM")
  expect_equal(funcTrim(" TRIM "),"TRIM")
  expect_equal(funcTrim("TRIM "),"TRIM")
  expect_equal(funcTrim("      TRIM          "),"TRIM")
  expect_equal(funcTrim("TR IM"),"TR IM")
  expect_equal(funcTrim(" TR IM"),"TR IM")
  expect_equal(funcTrim("  TR I M"),"TR I M")
  expect_equal(funcTrim(" TR IM "),"TR IM")
  expect_equal(funcTrim("T R IM "),"T R IM")
  expect_equal(funcTrim("      T RIM          "),"T RIM")
})

#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.
context("Test funcWrite")
#Answer files
c_sAnswerWriteFile1 = file.path(c_strCWD,c_strCorrectAnswers,"FuncWriteTemp1.txt")
c_sAnswerWriteFile2 = file.path(c_strCWD,c_strCorrectAnswers,"FuncWriteTemp2.txt")
print("c_sAnswerWriteFile2")
print(c_sAnswerWriteFile2)
c_sAnswerWriteDFFile1 = file.path(c_strCWD,c_strCorrectAnswers,"FuncWriteTempDF1.txt")
c_sAnswerWriteDFFile2 = file.path(c_strCWD,c_strCorrectAnswers,"FuncWriteTempDF2.txt")

#Working files
c_sTempWriteFile1 = file.path(c_strCWD,c_strTemporaryFiles,"FuncWriteTemp1.txt")
c_sTempWriteFile2 = file.path(c_strCWD,c_strTemporaryFiles,"FuncWriteTemp2.txt")
c_sTempWriteDFFile1 = file.path(c_strCWD,c_strTemporaryFiles,"FuncWriteTempDF1.txt")
c_sTempWriteDFFile2 = file.path(c_strCWD,c_strTemporaryFiles,"FuncWriteTempDF2.txt")
dfTest = as.data.frame(as.matrix(cbind(c(1,11,111),c(2,22,222),c(3,33,333))))
sWriteString = "Testing, 1,2,3 anything but that."
unlink(c_sTempWriteFile1)
unlink(c_sTempWriteFile2)
unlink(c_sTempWriteDFFile1)
unlink(c_sTempWriteDFFile2)
funcWrite(sWriteString,c_sTempWriteFile1)
funcWrite(sWriteString,c_sTempWriteFile2)
funcWrite(sWriteString,c_sTempWriteFile2)
funcWrite(dfTest,c_sTempWriteDFFile1)
funcWrite(dfTest,c_sTempWriteDFFile2)
funcWrite(dfTest,c_sTempWriteDFFile2)

test_that("Test that a test file is written and appended to for strings and dataframes.",{
  expect_equal(readLines(c_sTempWriteFile1),readLines(c_sAnswerWriteFile1))
  expect_equal(readLines(c_sTempWriteFile2),readLines(c_sAnswerWriteFile2))
  expect_equal(readLines(c_sTempWriteDFFile1),readLines(c_sAnswerWriteDFFile1))
  expect_equal(readLines(c_sTempWriteDFFile2),readLines(c_sAnswerWriteDFFile2))
})

context("Test funcWriteTable")
#Answer files
c_sAnswerWriteDFFile1 = file.path(c_strCWD,c_strCorrectAnswers,"FuncWriteTableTempDF1.txt")
c_sAnswerWriteDFFile2 = file.path(c_strCWD,c_strCorrectAnswers,"FuncWriteTableTempDF2.txt")

#Working files
c_sTempWriteDFFile1 = file.path(c_strCWD,c_strTemporaryFiles,"FuncWriteTableTempDF1.txt")
c_sTempWriteDFFile2 = file.path(c_strCWD,c_strTemporaryFiles,"FuncWriteTableTempDF2.txt")
unlink(c_sTempWriteDFFile1)
unlink(c_sTempWriteDFFile2)
funcWriteTable(dfTest,c_sTempWriteDFFile1)
funcWriteTable(dfTest,c_sTempWriteDFFile2, fAppend=TRUE)
funcWriteTable(dfTest,c_sTempWriteDFFile2, fAppend=TRUE)

test_that("Test that a test file is written and appended to for dataframes.",{
  expect_equal(readLines(c_sTempWriteDFFile1),readLines(c_sAnswerWriteDFFile1))
  expect_equal(readLines(c_sTempWriteDFFile2),readLines(c_sAnswerWriteDFFile2))
})

context("Test funcCoef2Col")
dfTestWithFactors = as.data.frame(as.matrix(cbind(c(1,11,111),c(2,22,222),c(3,33,333))))
colnames(dfTestWithFactors)=c("A","B","C")
dfTestWithFactors["B"]=as.factor(as.character(dfTestWithFactors[["B"]]))
test_that("Test that a coefficients are found or not given if they exist",{
  expect_equal(funcCoef2Col(strCoef="C",frmeData=dfTestWithFactors,astrCols=c()),"C")
  expect_equal(funcCoef2Col(strCoef="A",frmeData=dfTestWithFactors,astrCols=c()),"A")
  expect_equal(funcCoef2Col(strCoef=paste("B","2",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
  expect_equal(funcCoef2Col(strCoef=paste("B","22",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
  expect_equal(funcCoef2Col(strCoef=paste("B","222",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c()),"B")
  expect_equal(funcCoef2Col(strCoef="C",frmeData=dfTestWithFactors,astrCols=c("A","B","C")),"C")
  expect_equal(funcCoef2Col(strCoef=paste("B","2",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("A","B")),"B")
  expect_equal(funcCoef2Col(strCoef=paste("B","22",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("B","C")),"B")
  expect_equal(funcCoef2Col(strCoef=paste("B","222",sep=c_sFactorNameSep),frmeData=dfTestWithFactors,astrCols=c("B")),"B")
})

context("Test funcMFAValue2Col")
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"))
dfTestWithFactors["three"]=as.factor(dfTestWithFactors[["three"]])
test_that("Test that a column names is found or not given if they exist",{
  expect_equal(funcMFAValue2Col(xValue=5.8,dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"B")
  expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"A")
  expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"C")
  expect_equal(funcMFAValue2Col(xValue="two",dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"C")
  expect_equal(funcMFAValue2Col(xValue=paste("D","1",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"D")
  expect_equal(funcMFAValue2Col(xValue=paste("D","2",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=NULL),"D")
  expect_equal(funcMFAValue2Col(xValue=2.0,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,3)),NULL)
  expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(2,3)),NULL)
  expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,2)),NULL)
  expect_equal(funcMFAValue2Col(xValue="two",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1,2)),NULL)
  expect_equal(funcMFAValue2Col(xValue=2.0,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(2)),"B")
  expect_equal(funcMFAValue2Col(xValue=6,dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(1)),"A")
  expect_equal(funcMFAValue2Col(xValue="one",dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(3)),"C")
  expect_equal(funcMFAValue2Col(xValue=paste("D","2",sep=c_sMFANameSep1),dfData=dfTestWithFactors, aiColumnIndicesToSearch=c(4)),"D")
})

context("Test funcFormulaStrToList")
test_that("List of covariates are given, from lm or mixed model formulas",{
  expect_equal(funcFormulaStrToList("adCur ~ `1Covariate`"),c("1Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate`"),c("1Covariate","2Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate`"),c("1Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate`"),c("1Covariate","2Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + `2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + 1|`2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + 1|`2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + `2Covariate` + 1|`3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ 1|`1Covariate` + `2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
  expect_equal(funcFormulaStrToList("adCur ~ `1Covariate` + 1|`2Covariate` + `3Covariate`"),c("1Covariate","2Covariate","3Covariate"))
})

context("Test funcFormulaListToString")
test_that("The correct string formula for a lm or mixed model is created from a list of covariates",{
  expect_equal(funcFormulaListToString(NULL),c(NA,NA))
  expect_equal(funcFormulaListToString(c("1Covariate")),c("adCur ~ `1Covariate`",NA))
  expect_equal(funcFormulaListToString(c("1Covariate","2Covariate")),c("adCur ~ `1Covariate` + `2Covariate`",NA))
  expect_equal(funcFormulaListToString(c("1Covariate","2Covariate","3Covariate")),c("adCur ~ `1Covariate` + `2Covariate` + `3Covariate`",NA))
  expect_equal(funcFormulaListToString(c("1Covariate","2Covariate"),c("3Covariate")),c(NA,"adCur ~ `1Covariate` + `2Covariate` + 1|`3Covariate`"))
  expect_equal(funcFormulaListToString(c("1Covariate","3Covariate"),c("2Covariate")),c(NA,"adCur ~ `1Covariate` + `3Covariate` + 1|`2Covariate`"))
  expect_equal(funcFormulaListToString(c("2Covariate","3Covariate"),c("1Covariate")),c(NA,"adCur ~ `2Covariate` + `3Covariate` + 1|`1Covariate`"))
  expect_equal(funcFormulaListToString(c("2Covariate"),c("1Covariate","3Covariate")),c(NA,"adCur ~ `2Covariate` + 1|`1Covariate` + 1|`3Covariate`"))
  expect_equal(funcFormulaListToString(c("1Covariate"),c("2Covariate","3Covariate")),c(NA,"adCur ~ `1Covariate` + 1|`2Covariate` + 1|`3Covariate`"))
  expect_equal(funcFormulaListToString(c("3Covariate"),c("1Covariate","2Covariate")),c(NA,"adCur ~ `3Covariate` + 1|`1Covariate` + 1|`2Covariate`"))
})