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Update extractInformationWhenNoIntersection() function to use the Ens…
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…embl list rather than the query list
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@adeschen
adeschen committed Aug 12, 2024
1 parent 1121623 commit bdc5a4c
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Showing 2 changed files with 80 additions and 37 deletions.
3 changes: 2 additions & 1 deletion R/methodsInternal.R
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Original file line number Diff line number Diff line change
Expand Up @@ -445,7 +445,8 @@ extractInformationWhenNoIntersection <- function(gostResults, gostObject) {

query <- listQuery[1]

listGenes <- unique(gostObject$meta$query_metadata$queries[[query]])
## List of Ensembl genes
listGenes <- unique(gostObject$meta$genes_metadata$query[[query]]$ensgs)

## Extract information about the enriched terms from database
gostQuery <- gostResults[which(gostResults$query == query),]
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114 changes: 78 additions & 36 deletions tests/testthat/test-methodsInternal.R
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Original file line number Diff line number Diff line change
Expand Up @@ -354,7 +354,7 @@ test_that("extractInformationWhenNoIntersection() must return expected text", {
mirnaDemo <- demoGOST

mirnaDemo$meta$query_metadata$queries[[1]] <-
mirnaDemo$meta$query_metadata$queries[[1]][1:4]
mirnaDemo$meta$query_metadata$queries[[1]][1:3]

mirnaData <- demoGOST$result[demoGOST$result$source == "MIRNA", ]

Expand All @@ -365,32 +365,36 @@ test_that("extractInformationWhenNoIntersection() must return expected text", {
expected <- list()

expected[["geneNodes"]] <- data.frame("id"=c("ENSG00000059728",
"ENSG00000077616", "ENSG00000051108"),
group=rep("GENE", 3),
alias=c("MXD1", "NAALAD2", "HERPUD1"),
"ENSG00000077616", "ENSG00000100292", "ENSG00000107968",
"ENSG00000108551", "ENSG00000113369", "ENSG00000051108",
"ENSG00000087074", "ENSG00000105327"),
group=rep("GENE", 9),
alias=c("MXD1", "NAALAD2", "HMOX1", "MAP3K8", "RASD1",
"ARRDC3", "HERPUD1", "PPP1R15A", "BBC3"),
check.names=FALSE, stringsAsFactors=FALSE)

expected[["termNode"]] <- data.frame(id=c("MIRNA:hsa-miR-335-5p",
expected[["termNodes"]] <- data.frame(id=c("MIRNA:hsa-miR-335-5p",
"MIRNA:hsa-miR-3180-5p", "MIRNA:hsa-miR-759"),
target=c("ENSG00000059728", "ENSG00000077616",
"ENSG00000051108", "ENSG00000059728", "ENSG00000051108",
"ENSG00000059728"),
interaction=rep("contains", 6),
group=rep("TERM", 3),
alias=c("hsa-miR-335-5p",
"hsa-miR-3180-5p", "hsa-miR-759"),
check.names=FALSE, stringsAsFactors=FALSE)

expected[["edges"]] <- data.frame(
"source"=c("MIRNA:hsa-miR-335-5p", "MIRNA:hsa-miR-335-5p",
"MIRNA:hsa-miR-335-5p", "MIRNA:hsa-miR-3180-5p",
"MIRNA:hsa-miR-759", "MIRNA:hsa-miR-759"),
target=c("ENSG00000059728", "ENSG00000077616", "ENSG00000051108",
"ENSG00000059728", "ENSG00000051108", "ENSG00000059728"),
interaction=rep("contains", 6),
"source"=c(rep("MIRNA:hsa-miR-335-5p", 7),
rep("MIRNA:hsa-miR-3180-5p", 3),
rep("MIRNA:hsa-miR-759", 3)),
target=c("ENSG00000059728", "ENSG00000077616", "ENSG00000100292",
"ENSG00000107968", "ENSG00000108551", "ENSG00000113369",
"ENSG00000051108", "ENSG00000087074",
"ENSG00000100292", "ENSG00000059728", "ENSG00000051108",
"ENSG00000059728", "ENSG00000105327"),
interaction=rep("contains", 13),
check.names=FALSE, stringsAsFactors=FALSE)

expect_equal(result$nodes, expected$nodes)
expect_equal(result$geneNodes, expected$geneNodes)
expect_equal(result$termNodes, expected$termNodes)
expect_equal(result$edges, expected$edges)
expect_equal(result$nodeAttributes, expected$nodeAttributes)
expect_equal(result$edgeAttributes, expected$edgeAttributes)
})


Expand All @@ -413,27 +417,65 @@ test_that("createCXJSONForCytoscape() must return expected text", {
nodeEdgeInfo=info, title = "MIRNA")

expected <- paste0(
"[{\"metaData\":[{\"name\":\"nodes\",\"version\":\"1.0\"},",
"{\"name\":\"edges\",\"version\":\"1.0\"},{\"name\":\"edgeAttributes\",\"version\":\"1.0\"},",
"[{\"metaData\":[{\"name\":\"nodes\",\"version\":\"1.0\"},",
"{\"name\":\"edges\",\"version\":\"1.0\"},{\"name\":\"edgeAttributes\",",
"\"version\":\"1.0\"},{\"name\":\"nodeAttributes\",\"version\":\"1.0\"},",
"{\"name\":\"cyHiddenAttributes\",\"version\":\"1.0\"},",
"{\"name\":\"cyNetworkRelations\",\"version\":\"1.0\"},",
"{\"name\":\"cyGroups\",\"version\":\"1.0\"},{\"name\":\"networkAttributes\",\"version\":\"1.0\"},",
"{\"name\":\"cyTableColumn\",\"version\":\"1.0\"},{\"name\":\"cySubNetworks\",\"version\":\"1.0\"}]},",
"{\"networkAttributes\":[{\"n\":\"name\",\"v\":\"MIRNA\"}]},{\"nodes\":[{\"@id\":1,\"n\":\"ENSG00000059728\"},",
"{\"@id\":2,\"n\":\"ENSG00000077616\"},{\"@id\":3,\"n\":\"ENSG00000100292\"},{\"@id\":4,\"n\":\"ENSG00000107968\"},",
"{\"@id\":5,\"n\":\"ENSG00000108551\"},{\"@id\":6,\"n\":\"ENSG00000113369\"},{\"@id\":7,\"n\":\"ENSG00000051108\"},",
"{\"@id\":8,\"n\":\"ENSG00000087074\"},{\"@id\":9,\"n\":\"ENSG00000105327\"},{\"@id\":10,\"n\":\"MIRNA:hsa-miR-335-5p\"},",
"{\"@id\":11,\"n\":\"MIRNA:hsa-miR-3180-5p\"},{\"@id\":12,\"n\":\"MIRNA:hsa-miR-759\"}]},",
"{\"edges\":[{\"@id\":13,\"s\":11,\"t\":7,\"i\":\"contains\"},{\"@id\":14,\"s\":11,\"t\":7,\"i\":\"contains\"},",
"{\"@id\":15,\"s\":11,\"t\":1,\"i\":\"contains\"},{\"@id\":16,\"s\":10,\"t\":1,\"i\":\"contains\"},",
"{\"@id\":17,\"s\":10,\"t\":1,\"i\":\"contains\"},{\"@id\":18,\"s\":10,\"t\":2,\"i\":\"contains\"},",
"{\"@id\":19,\"s\":10,\"t\":8,\"i\":\"contains\"},{\"@id\":20,\"s\":10,\"t\":3,\"i\":\"contains\"},",
"{\"@id\":21,\"s\":10,\"t\":3,\"i\":\"contains\"},{\"@id\":22,\"s\":10,\"t\":9,\"i\":\"contains\"},",
"{\"@id\":23,\"s\":12,\"t\":4,\"i\":\"contains\"},{\"@id\":24,\"s\":12,\"t\":5,\"i\":\"contains\"},",
"{\"@id\":25,\"s\":12,\"t\":6,\"i\":\"contains\"}]},{\"nodeAttributes\":[{\"po\":1,\"n\":\"alias\",\"v\":\"MXD1\"},",
"{\"po\":2,\"n\":\"alias\",\"v\":\"NAALAD2\"},{\"po\":3,\"n\":\"alias\",\"v\":\"HMOX1\"},",
"{\"po\":4,\"n\":\"alias\",\"v\":\"MAP3K8\"},{\"po\":5,\"n\":\"alias\",\"v\":\"RASD1\"},",
"{\"po\":6,\"n\":\"alias\",\"v\":\"ARRDC3\"},{\"po\":7,\"n\":\"alias\",\"v\":\"HERPUD1\"},",
"{\"po\":8,\"n\":\"alias\",\"v\":\"PPP1R15A\"},{\"po\":9,\"n\":\"alias\",\"v\":\"BBC3\"},",
"{\"po\":1,\"n\":\"group\",\"v\":\"GENE\"},{\"po\":2,\"n\":\"group\",\"v\":\"GENE\"},{\"po\":3,\"n\":\"group\",\"v\":\"GENE\"},",
"{\"po\":4,\"n\":\"group\",\"v\":\"GENE\"},{\"po\":5,\"n\":\"group\",\"v\":\"GENE\"},{\"po\":6,\"n\":\"group\",\"v\":\"GENE\"},",
"{\"po\":7,\"n\":\"group\",\"v\":\"GENE\"},{\"po\":8,\"n\":\"group\",\"v\":\"GENE\"},{\"po\":9,\"n\":\"group\",\"v\":\"GENE\"},",
"{\"po\":10,\"n\":\"alias\",\"v\":\"hsa-miR-335-5p\"},{\"po\":11,\"n\":\"alias\",\"v\":\"hsa-miR-3180-5p\"},",
"{\"po\":12,\"n\":\"alias\",\"v\":\"hsa-miR-759\"},{\"po\":10,\"n\":\"group\",\"v\":\"TERM\"},",
"{\"po\":11,\"n\":\"group\",\"v\":\"TERM\"},{\"po\":12,\"n\":\"group\",\"v\":\"TERM\"}]},",
"{\"edgeAttributes\":[{\"po\":13,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-335-5p (contains) ENSG00000059728\"},",
"{\"po\":14,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-335-5p (contains) ENSG00000077616\"},",
"{\"po\":15,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-335-5p (contains) ENSG00000100292\"},",
"{\"po\":16,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-335-5p (contains) ENSG00000107968\"},",
"{\"po\":17,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-335-5p (contains) ENSG00000108551\"},",
"{\"po\":18,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-335-5p (contains) ENSG00000113369\"},",
"{\"po\":19,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-335-5p (contains) ENSG00000051108\"},",
"{\"po\":20,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-3180-5p (contains) ENSG00000087074\"},",
"{\"po\":21,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-3180-5p (contains) ENSG00000100292\"},",
"{\"po\":22,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-3180-5p (contains) ENSG00000059728\"},",
"{\"po\":23,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-759 (contains) ENSG00000051108\"},",
"{\"po\":24,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-759 (contains) ENSG00000059728\"},",
"{\"po\":25,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-759 (contains) ENSG00000105327\"},{\"po\":13,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-335-5p\"},",
"{\"po\":14,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-335-5p\"},{\"po\":15,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-335-5p\"},",
"{\"po\":16,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-335-5p\"},{\"po\":17,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-335-5p\"},",
"{\"po\":18,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-335-5p\"},{\"po\":19,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-335-5p\"},",
"{\"po\":20,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-3180-5p\"},{\"po\":21,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-3180-5p\"},",
"{\"po\":22,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-3180-5p\"},{\"po\":23,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-759\"},",
"{\"po\":24,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-759\"},{\"po\":25,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-759\"},",
"{\"po\":13,\"n\":\"target\",\"v\":\"ENSG00000059728\"},{\"po\":14,\"n\":\"target\",\"v\":\"ENSG00000077616\"},",
"{\"po\":15,\"n\":\"target\",\"v\":\"ENSG00000100292\"},{\"po\":16,\"n\":\"target\",\"v\":\"ENSG00000107968\"},",
"{\"po\":17,\"n\":\"target\",\"v\":\"ENSG00000108551\"},{\"po\":18,\"n\":\"target\",\"v\":\"ENSG00000113369\"},",
"{\"po\":19,\"n\":\"target\",\"v\":\"ENSG00000051108\"},{\"po\":20,\"n\":\"target\",\"v\":\"ENSG00000087074\"},",
"{\"po\":21,\"n\":\"target\",\"v\":\"ENSG00000100292\"},{\"po\":22,\"n\":\"target\",\"v\":\"ENSG00000059728\"},",
"{\"po\":23,\"n\":\"target\",\"v\":\"ENSG00000051108\"},{\"po\":24,\"n\":\"target\",\"v\":\"ENSG00000059728\"},",
"{\"po\":25,\"n\":\"target\",\"v\":\"ENSG00000105327\"}]},{\"cyHiddenAttributes\":[{\"n\":\"layoutAlgorithm\",\"y\":\"yFiles Circular Layout\"}]},",
"{\"metaData\":[{\"name\":\"nodes\",\"version\":\"1.0\"},{\"name\":\"edges\",\"version\":\"1.0\"},{\"name\":\"edgeAttributes\",\"version\":\"1.0\"},",
"{\"name\":\"nodeAttributes\",\"version\":\"1.0\"},{\"name\":\"cyHiddenAttributes\",\"version\":\"1.0\"},",
"{\"name\":\"cyNetworkRelations\",\"version\":\"1.0\"},{\"name\":\"cyGroups\",\"version\":\"1.0\"},",
"{\"name\":\"networkAttributes\",\"version\":\"1.0\"},{\"name\":\"cyTableColumn\",\"version\":\"1.0\"},",
"{\"name\":\"cySubNetworks\",\"version\":\"1.0\"}]},{\"networkAttributes\":[{\"n\":\"name\",\"v\":\"MIRNA\"}]},",
"{\"nodes\":[{\"@id\":1,\"n\":\"ENSG00000051108\"},{\"@id\":2,\"n\":\"MIRNA:hsa-miR-335-5p\"},{\"@id\":3,\"n\":\"MIRNA:hsa-miR-759\"}]},",
"{\"edges\":[{\"@id\":4,\"s\":2,\"t\":1,\"i\":\"contains\"},{\"@id\":5,\"s\":3,\"t\":1,\"i\":\"contains\"}]},",
"{\"nodeAttributes\":[{\"po\":1,\"n\":\"alias\",\"v\":\"HERPUD1\"},{\"po\":1,\"n\":\"group\",\"v\":\"GENE\"},",
"{\"po\":2,\"n\":\"alias\",\"v\":\"hsa-miR-335-5p\"},{\"po\":3,\"n\":\"alias\",\"v\":\"hsa-miR-759\"},",
"{\"po\":2,\"n\":\"group\",\"v\":\"TERM\"},{\"po\":3,\"n\":\"group\",\"v\":\"TERM\"}]},",
"{\"edgeAttributes\":[{\"po\":4,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-335-5p (contains) ENSG00000051108\"},",
"{\"po\":5,\"n\":\"name\",\"v\":\"MIRNA:hsa-miR-759 (contains) ENSG00000051108\"},",
"{\"po\":4,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-335-5p\"},{\"po\":5,\"n\":\"source\",\"v\":\"MIRNA:hsa-miR-759\"},",
"{\"po\":4,\"n\":\"target\",\"v\":\"ENSG00000051108\"},{\"po\":5,\"n\":\"target\",\"v\":\"ENSG00000051108\"}]},",
"{\"cyHiddenAttributes\":[{\"n\":\"layoutAlgorithm\",\"y\":\"yFiles Circular Layout\"}]},",
"{\"metaData\":[{\"name\":\"nodes\",\"version\":\"1.0\"},{\"name\":\"edges\",\"version\":\"1.0\"},",
"{\"name\":\"edgeAttributes\",\"version\":\"1.0\"},{\"name\":\"nodeAttributes\",\"version\":\"1.0\"},",
"{\"name\":\"cyHiddenAttributes\",\"version\":\"1.0\"},{\"name\":\"cyNetworkRelations\",\"version\":\"1.0\"},",
"{\"name\":\"cyGroups\",\"version\":\"1.0\"},{\"name\":\"networkAttributes\",\"version\":\"1.0\"},",
"{\"name\":\"cyTableColumn\",\"version\":\"1.0\"},",
"{\"name\":\"cySubNetworks\",\"version\":\"1.0\"}]},{\"status\":[{\"error\":\"\",\"success\":true}]}]")

expect_equal(result, expected)
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