tests/testthat/test-methodsEmap.R
In adeschen/gprofiler2cytoscape: From functional enrichment results to biological networks
### Unit tests for methodsEmap.R functions
library(enrichViewNet)
data(demoGOST)
### Tests createEnrichMap() results
context("createEnrichMap() results")
test_that("createEnrichMap() must return error when gostObject is a number", {
error_message <- paste0("The gostObject object should be a list ",
"with meta and result as entries corresponding ",
"to gprofiler2 enrichment output.")
expect_error(createEnrichMap(gostObject=33, query="TEST",
source="GO:CC", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when gostObject is a string character", {
error_message <- paste0("The gostObject object should be a list ",
"with meta and result as entries corresponding ",
"to gprofiler2 enrichment output.")
expect_error(createEnrichMap(gostObject="TEST", query="TEST",
source="GO:CC", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when query is a number", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
error_message <- paste0("The \'query\'must be a character string.")
expect_error(createEnrichMap(gostObject=gostObject, query=33,
source="KEGG", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when query is a vector of strings", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
error_message <- paste0("The \'query\'must be a character string.")
expect_error(createEnrichMap(gostObject=gostObject, query=c("1", "2"),
source="KEGG", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when query is not in gost", {
error_message <- paste0("The \'query\' is not present in the ",
"results of the gost object.")
expect_error(createEnrichMap(gostObject=demoGOST, query="CANADA",
source="KEGG", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when source is a number", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
error_message <- paste0("Assertion on 'arg' failed: Must be of type ",
"'character', not 'double'.")
expect_error(createEnrichMap(gostObject=gostObject, query="toto",
source=333, termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when source is a wrong name", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
expect_error(createEnrichMap(gostObject=gostObject, query="toto",
source="test", termIDs=NULL, removeRoot=TRUE, title="network",
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1))
})
test_that("createEnrichMap() must return error when source is GO", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
expect_error(createEnrichMap(gostObject=gostObject, query="toto",
source="GO",
termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1))
})
test_that("createEnrichMap() must return error when removeRoot remove last enriched term", {
gostTerm <- demoGOST
gostTerm$result <- demoGOST$result[54,]
error_message <- paste0("With removal of the root term, there is no ",
"enrichment term left")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when removeRoot remove last enriched term from term list", {
gostTerm <- demoGOST
gostTerm$result <- demoGOST$result[54,]
error_message <- paste0("With removal of the root term, there is no ",
"enrichment term left")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="TERM_ID",
termIDs=c("WP:000000"), removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when showCategory negative value", {
gostTerm <- demoGOST
error_message <- paste0("The \'showCategory\' parameter must an positive ",
"integer or a vector of character strings representing terms.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=-30,
groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=2), error_message)
})
test_that("createEnrichMap() must return error when showCategory is boolean", {
gostTerm <- demoGOST
error_message <- paste0("The \'showCategory\' parameter must an positive ",
"integer or a vector of character strings representing terms.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=TRUE,
groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when groupCategory is integer", {
gostTerm <- demoGOST
error_message <- paste0("The \'groupCategory\' parameter must a logical ",
"(TRUE or FALSE).")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=22, categoryLabel=1,
categoryNode=1, line=1), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when categoryLabel is string", {
gostTerm <- demoGOST
error_message <- paste0("The \'categoryLabel\' parameter ",
"must be a positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel="test",
categoryNode=1, line=2), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when cexLabelCategory is negative", {
gostTerm <- demoGOST
error_message <- paste0("The \'categoryLabel\' parameter ",
"must be a positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=-1.1,
categoryNode=1, line=2), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when categoryNode is negative", {
gostTerm <- demoGOST
error_message <- paste0("The \'categoryNode\' parameter ",
"must be a positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=2,
categoryNode=-1), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when categoryNode is string", {
gostTerm <- demoGOST
error_message <- paste0("The \'categoryNode\' parameter ",
"must be a positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=2,
categoryNode="te", line=1), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when line is a string", {
gostTerm <- demoGOST
error_message <- paste0("The \'line\' parameter must be a ",
"positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1, line="HI"),
error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when line is a negative number", {
gostTerm <- demoGOST
error_message <- paste0("The \'line\' parameter must be a ",
"positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1, line=-0.3),
error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when not term for selected source", {
gostTerm <- demoGOST
gostTerm$result <- gostTerm$result[gostTerm$result$source != "WP", ]
error_message <- paste0("There is no enriched term for the selected ",
"source \'WP'.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1, line=1), error_message,
fixed=TRUE)
})
test_that("createEnrichMap() must return error when not term id and TERM_ID selected", {
gostTerm <- demoGOST
error_message <- paste0("A vector of terms should be given through the ",
"\'termIDs\' parameter when source is \'TERM_ID\'.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="TERM_ID", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=1, categoryNode=1, line=1),
error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when not all term ids are present", {
gostTerm <- demoGOST
error_message <- paste0("Not all listed terms are present in the ",
"enrichment results.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="TERM_ID", termIDs = c("GO:0051173", "GO:0065004", "GO:1905898"),
removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=1, categoryNode=1, line=1),
error_message, fixed=TRUE)
})
### Tests createEnrichMapMultiBasic() results
context("createEnrichMapMultiBasic() results")
test_that("createEnrichMapMultiBasic() must return error when gostObjectList is a number", {
error_message <- paste0("The gostObjectList object should be a list ",
"of enrichment objects. At least 2 enrichment objects are required.")
expect_error(createEnrichMapMultiBasic(gostObjectList=33,
queryList=c("TEST", "Test2"), source="GO:CC", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMapMultiBasic() must return error when gostObjectList has only one element", {
gostTerm <- demoGOST
error_message <- paste0("The gostObjectList object should be a list ",
"of enrichment objects. At least 2 enrichment objects are required.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm),
queryList=list("TEST"), source="GO:CC", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message)
})
test_that("createEnrichMapMultiBasic() must return error when queryList is a number", {
gostTerm <- demoGOST
error_message <- paste0("The queryList object should be a list of query ",
"names. At least 2 query names are required. The number of query ",
"names should correspond to the number of enrichment objects.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=33, source="GO:CC", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message)
})
test_that("createEnrichMapMultiBasic() must return error when queryList is longer than gostObjectList", {
gostTerm <- demoGOST
error_message <- paste0("The queryList object should be a list of query ",
"names. At least 2 query names are required. The number of query ",
"names should correspond to the number of enrichment objects.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("TEST", "TEST2", "TEST3"), source="GO:CC", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message)
})
test_that("createEnrichMapMultiBasic() must return error when one query in queryList is not in gostObject", {
gostTerm <- demoGOST
error_message <- paste0("Each query name present in the ",
"\'queryList\' parameter must be present in the associated ",
"enrichment object.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("query_1", "TEST"), source="GO:CC", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiBasic() must return error when one object in gostObjectList in a number", {
gostTerm <- demoGOST
error_message <- paste0("The gostObjectList should only contain a list ",
"of enrichment results. Enrichment results are lists with meta ",
"and result as entries corresponding to gprofiler2 ",
"enrichment output.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, 33),
queryList=list("query_1", "query_1"), source="GO:CC", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiBasic() must return error when no enriched term for selected source", {
gostTerm <- demoGOST
gostTerm$result <- gostTerm$result[which(gostTerm$result$source != "WP"), ]
error_message <- paste0("There is no enriched term for the selected ",
"source \'WP\'.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("query_1", "query_1"), source="WP", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiBasic() must return error when number in queryList", {
gostTerm <- demoGOST
error_message <- paste0("The queryList object should only contain a list ",
"of query names in character strings.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("query_1", 33), source="WP", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiBasic() must return error when number in queryList", {
gostTerm <- demoGOST
error_message <- paste0("A vector of terms should be given through the ",
"\'termIDs\' parameter when source is \'TERM_ID\'.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("query_1", "query_1"), source="TERM_ID", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
### Tests createEnrichMapMultiComplex() results
context("createEnrichMapMultiComplex() results")
test_that("createEnrichMapMultiComplex() must return error when gostObjectList is a number", {
error_message <- paste0("The gostObjectList object should be a list ",
"of enrichment objects. At least 2 enrichment objects are required.")
queryDF <- data.frame(queryName=c("parental_napa_vs_DMSO",
"rosa_napa_vs_DMSO", "rosa_napa_vs_DMSO"),
source=c("GO:CC", "REAC", "GO:CC"), removeRoot=c(TRUE, TRUE, TRUE),
termIDs=c("", "", ""), stringsAsFactors=FALSE)
expect_error(createEnrichMapMultiComplex(gostObjectList=33,
queryInfo=queryDF, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1, line=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when gostObjectList has only one element", {
gostTerm <- demoGOST
queryDF <- data.frame(queryName=c("query_1"),
source=c("GO:CC"), removeRoot=c(TRUE),
termIDs=c(""), stringsAsFactors=FALSE)
error_message <- paste0("The gostObjectList object should be a list ",
"of enrichment objects. At least 2 enrichment objects are required.")
expect_error(createEnrichMapMultiComplex(gostObjectList=list(gostTerm),
queryInfo=queryDF, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when gostObjectList is a list of numbers", {
error_message <- paste0("The gostObjectList should only contain a list ",
"of enrichment results. Enrichment results are lists with meta and",
" result as entries corresponding to gprofiler2 enrichment",
" output.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(3, 4),
queryInfo=33, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when queryInfo is a number", {
gostTerm <- demoGOST
error_message <- paste0("The queryInfo should a data.frame with ",
"those columns: queryName, source, removeRoot and termIDs.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=33, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when queryInfo shorter than gostObjectList", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1"),
source=c("KEGG"), removeRoot=c(TRUE), termIDs=c(""),
stringsAsFactors=FALSE)
error_message <- paste0("The number of rows in queryInfo should ",
" correspond to the number of enrichment objects.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when source in queryInfo is not in list of sources", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "TEST"), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The values in the \'source\' column of the \'queryInfo\' ",
"data frame should be one of those: \"TERM_ID\", \"GO:MF\", ",
"\"GO:CC\", \"GO:BP\", \"KEGG\", \"REAC\", \"TF\", ",
"\"MIRNA\", \"HPA\", \"CORUM\", \"HP\", \"WP\".")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when source in queryInfo is number", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c(33, 22), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The \'source'\ column of the \'queryInfo\' ",
"data frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when queryName in queryInfo is number", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c(22, 33),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The \'queryName'\ column of the \'queryInfo\' ",
"data frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when termIDs in queryInfo is number", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE), termIDs=c(33, 22),
stringsAsFactors=FALSE)
error_message <- paste0("The \'termIDs'\ column of the \'queryInfo\' ",
"data frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when removeRoot in queryInfo is number", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "REAC"), removeRoot=c(33, 22), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The \'removeRoot'\ column of the \'queryInfo\' ",
"data frame should only contain logical values (TRUE or FALSE).")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when query name in queryInfo not in enrichment object", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_2"),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("Each query name present in the \'queryName'\ ",
"column of the \'queryInfo\' data frame must be present in the ",
"associated enrichment object.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when TERM_ID in queryInfo but not term ids", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "TERM_ID"), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("A string of terms should be present in the ",
"\'termIDs\' column when source is \'TERM_ID\'.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when termIDs column in queryInfo contains numbers", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "TERM_ID"), removeRoot=c(TRUE, TRUE), termIDs=c(33, 22),
stringsAsFactors=FALSE)
error_message <- paste0("The \'termIDs\' column of the 'queryInfo' data ",
"frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message,
fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when removeRoot column in queryInfo contains numbers", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "TERM_ID"), removeRoot=c(33, 22), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The \'removeRoot\' column of the 'queryInfo' ",
"data frame should only contain logical values (TRUE or FALSE).")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message,
fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when groupName column in queryInfo contains numbers", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE),
termIDs=c("", ""), groupName=c(22, 33),
stringsAsFactors=FALSE)
error_message <- paste0("The \'groupName\' column of the 'queryInfo' ",
"data frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message,
fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when groupName column contain identical names", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE),
termIDs=c("", ""), groupName=c("REAC", "REAC"),
stringsAsFactors=FALSE)
error_message <- paste0("The \'groupName\' column of the 'queryInfo' ",
"data frame should only contain unique group names.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message,
fixed=TRUE)
})
adeschen/gprofiler2cytoscape documentation built on Nov. 4, 2024, 3:16 p.m.
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### Unit tests for methodsEmap.R functions
library(enrichViewNet)
data(demoGOST)
### Tests createEnrichMap() results
context("createEnrichMap() results")
test_that("createEnrichMap() must return error when gostObject is a number", {
error_message <- paste0("The gostObject object should be a list ",
"with meta and result as entries corresponding ",
"to gprofiler2 enrichment output.")
expect_error(createEnrichMap(gostObject=33, query="TEST",
source="GO:CC", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when gostObject is a string character", {
error_message <- paste0("The gostObject object should be a list ",
"with meta and result as entries corresponding ",
"to gprofiler2 enrichment output.")
expect_error(createEnrichMap(gostObject="TEST", query="TEST",
source="GO:CC", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when query is a number", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
error_message <- paste0("The \'query\'must be a character string.")
expect_error(createEnrichMap(gostObject=gostObject, query=33,
source="KEGG", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when query is a vector of strings", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
error_message <- paste0("The \'query\'must be a character string.")
expect_error(createEnrichMap(gostObject=gostObject, query=c("1", "2"),
source="KEGG", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when query is not in gost", {
error_message <- paste0("The \'query\' is not present in the ",
"results of the gost object.")
expect_error(createEnrichMap(gostObject=demoGOST, query="CANADA",
source="KEGG", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when source is a number", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
error_message <- paste0("Assertion on 'arg' failed: Must be of type ",
"'character', not 'double'.")
expect_error(createEnrichMap(gostObject=gostObject, query="toto",
source=333, termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when source is a wrong name", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
expect_error(createEnrichMap(gostObject=gostObject, query="toto",
source="test", termIDs=NULL, removeRoot=TRUE, title="network",
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1))
})
test_that("createEnrichMap() must return error when source is GO", {
gostObject <- list()
gostObject[["meta"]] <- list()
gostObject[["result"]] <- list()
expect_error(createEnrichMap(gostObject=gostObject, query="toto",
source="GO",
termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1))
})
test_that("createEnrichMap() must return error when removeRoot remove last enriched term", {
gostTerm <- demoGOST
gostTerm$result <- demoGOST$result[54,]
error_message <- paste0("With removal of the root term, there is no ",
"enrichment term left")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when removeRoot remove last enriched term from term list", {
gostTerm <- demoGOST
gostTerm$result <- demoGOST$result[54,]
error_message <- paste0("With removal of the root term, there is no ",
"enrichment term left")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="TERM_ID",
termIDs=c("WP:000000"), removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when showCategory negative value", {
gostTerm <- demoGOST
error_message <- paste0("The \'showCategory\' parameter must an positive ",
"integer or a vector of character strings representing terms.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=-30,
groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=2), error_message)
})
test_that("createEnrichMap() must return error when showCategory is boolean", {
gostTerm <- demoGOST
error_message <- paste0("The \'showCategory\' parameter must an positive ",
"integer or a vector of character strings representing terms.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=TRUE,
groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMap() must return error when groupCategory is integer", {
gostTerm <- demoGOST
error_message <- paste0("The \'groupCategory\' parameter must a logical ",
"(TRUE or FALSE).")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=22, categoryLabel=1,
categoryNode=1, line=1), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when categoryLabel is string", {
gostTerm <- demoGOST
error_message <- paste0("The \'categoryLabel\' parameter ",
"must be a positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel="test",
categoryNode=1, line=2), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when cexLabelCategory is negative", {
gostTerm <- demoGOST
error_message <- paste0("The \'categoryLabel\' parameter ",
"must be a positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=-1.1,
categoryNode=1, line=2), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when categoryNode is negative", {
gostTerm <- demoGOST
error_message <- paste0("The \'categoryNode\' parameter ",
"must be a positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=2,
categoryNode=-1), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when categoryNode is string", {
gostTerm <- demoGOST
error_message <- paste0("The \'categoryNode\' parameter ",
"must be a positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=2,
categoryNode="te", line=1), error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when line is a string", {
gostTerm <- demoGOST
error_message <- paste0("The \'line\' parameter must be a ",
"positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1, line="HI"),
error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when line is a negative number", {
gostTerm <- demoGOST
error_message <- paste0("The \'line\' parameter must be a ",
"positive numeric.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1, line=-0.3),
error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when not term for selected source", {
gostTerm <- demoGOST
gostTerm$result <- gostTerm$result[gostTerm$result$source != "WP", ]
error_message <- paste0("There is no enriched term for the selected ",
"source \'WP'.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="WP", removeRoot=TRUE, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1, line=1), error_message,
fixed=TRUE)
})
test_that("createEnrichMap() must return error when not term id and TERM_ID selected", {
gostTerm <- demoGOST
error_message <- paste0("A vector of terms should be given through the ",
"\'termIDs\' parameter when source is \'TERM_ID\'.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="TERM_ID", removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=1, categoryNode=1, line=1),
error_message, fixed=TRUE)
})
test_that("createEnrichMap() must return error when not all term ids are present", {
gostTerm <- demoGOST
error_message <- paste0("Not all listed terms are present in the ",
"enrichment results.")
expect_error(createEnrichMap(gostObject=gostTerm, query="query_1",
source="TERM_ID", termIDs = c("GO:0051173", "GO:0065004", "GO:1905898"),
removeRoot=TRUE, showCategory=30,
groupCategory=FALSE, categoryLabel=1, categoryNode=1, line=1),
error_message, fixed=TRUE)
})
### Tests createEnrichMapMultiBasic() results
context("createEnrichMapMultiBasic() results")
test_that("createEnrichMapMultiBasic() must return error when gostObjectList is a number", {
error_message <- paste0("The gostObjectList object should be a list ",
"of enrichment objects. At least 2 enrichment objects are required.")
expect_error(createEnrichMapMultiBasic(gostObjectList=33,
queryList=c("TEST", "Test2"), source="GO:CC", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1, line=1), error_message)
})
test_that("createEnrichMapMultiBasic() must return error when gostObjectList has only one element", {
gostTerm <- demoGOST
error_message <- paste0("The gostObjectList object should be a list ",
"of enrichment objects. At least 2 enrichment objects are required.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm),
queryList=list("TEST"), source="GO:CC", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message)
})
test_that("createEnrichMapMultiBasic() must return error when queryList is a number", {
gostTerm <- demoGOST
error_message <- paste0("The queryList object should be a list of query ",
"names. At least 2 query names are required. The number of query ",
"names should correspond to the number of enrichment objects.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=33, source="GO:CC", termIDs=NULL, removeRoot=TRUE,
showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message)
})
test_that("createEnrichMapMultiBasic() must return error when queryList is longer than gostObjectList", {
gostTerm <- demoGOST
error_message <- paste0("The queryList object should be a list of query ",
"names. At least 2 query names are required. The number of query ",
"names should correspond to the number of enrichment objects.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("TEST", "TEST2", "TEST3"), source="GO:CC", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message)
})
test_that("createEnrichMapMultiBasic() must return error when one query in queryList is not in gostObject", {
gostTerm <- demoGOST
error_message <- paste0("Each query name present in the ",
"\'queryList\' parameter must be present in the associated ",
"enrichment object.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("query_1", "TEST"), source="GO:CC", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiBasic() must return error when one object in gostObjectList in a number", {
gostTerm <- demoGOST
error_message <- paste0("The gostObjectList should only contain a list ",
"of enrichment results. Enrichment results are lists with meta ",
"and result as entries corresponding to gprofiler2 ",
"enrichment output.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, 33),
queryList=list("query_1", "query_1"), source="GO:CC", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiBasic() must return error when no enriched term for selected source", {
gostTerm <- demoGOST
gostTerm$result <- gostTerm$result[which(gostTerm$result$source != "WP"), ]
error_message <- paste0("There is no enriched term for the selected ",
"source \'WP\'.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("query_1", "query_1"), source="WP", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiBasic() must return error when number in queryList", {
gostTerm <- demoGOST
error_message <- paste0("The queryList object should only contain a list ",
"of query names in character strings.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("query_1", 33), source="WP", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiBasic() must return error when number in queryList", {
gostTerm <- demoGOST
error_message <- paste0("A vector of terms should be given through the ",
"\'termIDs\' parameter when source is \'TERM_ID\'.")
expect_error(createEnrichMapMultiBasic(gostObjectList=list(gostTerm, gostTerm),
queryList=list("query_1", "query_1"), source="TERM_ID", termIDs=NULL,
removeRoot=TRUE, showCategory=30, groupCategory=FALSE, categoryLabel=1,
categoryNode=1), error_message, fixed=TRUE)
})
### Tests createEnrichMapMultiComplex() results
context("createEnrichMapMultiComplex() results")
test_that("createEnrichMapMultiComplex() must return error when gostObjectList is a number", {
error_message <- paste0("The gostObjectList object should be a list ",
"of enrichment objects. At least 2 enrichment objects are required.")
queryDF <- data.frame(queryName=c("parental_napa_vs_DMSO",
"rosa_napa_vs_DMSO", "rosa_napa_vs_DMSO"),
source=c("GO:CC", "REAC", "GO:CC"), removeRoot=c(TRUE, TRUE, TRUE),
termIDs=c("", "", ""), stringsAsFactors=FALSE)
expect_error(createEnrichMapMultiComplex(gostObjectList=33,
queryInfo=queryDF, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1, line=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when gostObjectList has only one element", {
gostTerm <- demoGOST
queryDF <- data.frame(queryName=c("query_1"),
source=c("GO:CC"), removeRoot=c(TRUE),
termIDs=c(""), stringsAsFactors=FALSE)
error_message <- paste0("The gostObjectList object should be a list ",
"of enrichment objects. At least 2 enrichment objects are required.")
expect_error(createEnrichMapMultiComplex(gostObjectList=list(gostTerm),
queryInfo=queryDF, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when gostObjectList is a list of numbers", {
error_message <- paste0("The gostObjectList should only contain a list ",
"of enrichment results. Enrichment results are lists with meta and",
" result as entries corresponding to gprofiler2 enrichment",
" output.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(3, 4),
queryInfo=33, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when queryInfo is a number", {
gostTerm <- demoGOST
error_message <- paste0("The queryInfo should a data.frame with ",
"those columns: queryName, source, removeRoot and termIDs.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=33, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when queryInfo shorter than gostObjectList", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1"),
source=c("KEGG"), removeRoot=c(TRUE), termIDs=c(""),
stringsAsFactors=FALSE)
error_message <- paste0("The number of rows in queryInfo should ",
" correspond to the number of enrichment objects.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when source in queryInfo is not in list of sources", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "TEST"), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The values in the \'source\' column of the \'queryInfo\' ",
"data frame should be one of those: \"TERM_ID\", \"GO:MF\", ",
"\"GO:CC\", \"GO:BP\", \"KEGG\", \"REAC\", \"TF\", ",
"\"MIRNA\", \"HPA\", \"CORUM\", \"HP\", \"WP\".")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when source in queryInfo is number", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c(33, 22), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The \'source'\ column of the \'queryInfo\' ",
"data frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when queryName in queryInfo is number", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c(22, 33),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The \'queryName'\ column of the \'queryInfo\' ",
"data frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when termIDs in queryInfo is number", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE), termIDs=c(33, 22),
stringsAsFactors=FALSE)
error_message <- paste0("The \'termIDs'\ column of the \'queryInfo\' ",
"data frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message)
})
test_that("createEnrichMapMultiComplex() must return error when removeRoot in queryInfo is number", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "REAC"), removeRoot=c(33, 22), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The \'removeRoot'\ column of the \'queryInfo\' ",
"data frame should only contain logical values (TRUE or FALSE).")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when query name in queryInfo not in enrichment object", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_2"),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("Each query name present in the \'queryName'\ ",
"column of the \'queryInfo\' data frame must be present in the ",
"associated enrichment object.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when TERM_ID in queryInfo but not term ids", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "TERM_ID"), removeRoot=c(TRUE, TRUE), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("A string of terms should be present in the ",
"\'termIDs\' column when source is \'TERM_ID\'.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message, fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when termIDs column in queryInfo contains numbers", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "TERM_ID"), removeRoot=c(TRUE, TRUE), termIDs=c(33, 22),
stringsAsFactors=FALSE)
error_message <- paste0("The \'termIDs\' column of the 'queryInfo' data ",
"frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message,
fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when removeRoot column in queryInfo contains numbers", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "TERM_ID"), removeRoot=c(33, 22), termIDs=c("", ""),
stringsAsFactors=FALSE)
error_message <- paste0("The \'removeRoot\' column of the 'queryInfo' ",
"data frame should only contain logical values (TRUE or FALSE).")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message,
fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when groupName column in queryInfo contains numbers", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE),
termIDs=c("", ""), groupName=c(22, 33),
stringsAsFactors=FALSE)
error_message <- paste0("The \'groupName\' column of the 'queryInfo' ",
"data frame should be in a character string format.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message,
fixed=TRUE)
})
test_that("createEnrichMapMultiComplex() must return error when groupName column contain identical names", {
gostTerm <- demoGOST
queryDataFrame <- data.frame(queryName=c("query_1", "query_1"),
source=c("KEGG", "REAC"), removeRoot=c(TRUE, TRUE),
termIDs=c("", ""), groupName=c("REAC", "REAC"),
stringsAsFactors=FALSE)
error_message <- paste0("The \'groupName\' column of the 'queryInfo' ",
"data frame should only contain unique group names.")
expect_error(createEnrichMapMultiComplex(
gostObjectList=list(gostTerm, gostTerm),
queryInfo=queryDataFrame, showCategory=30, groupCategory=FALSE,
categoryLabel=1, categoryNode=1), error_message,
fixed=TRUE)
})
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