## ----global_options, include=TRUE----------------------------------------
knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE, error = TRUE)
## ---- results = 'asis'---------------------------------------------------
pathToFileWithLipidomicsData <- paste(
find.package("ONION"),
"/example/nm-lipidomics.txt",
sep = "")
lipidomicsInputData <- read.table(pathToFileWithLipidomicsData, header = TRUE)
lipidomicsInputDf <- head(lipidomicsInputData, 6)
knitr::kable(lipidomicsInputDf[1:7], caption = "Lipidomisc data")
pathToFileWithTranscriptomicsData <- paste(
find.package("ONION"),
"/example/nm-transcriptomics.txt",
sep = "")
transcriptomicsInputData <- read.table(pathToFileWithTranscriptomicsData, header = TRUE)
transcriptomicsInputDf <- head(transcriptomicsInputData, 6)
knitr::kable(transcriptomicsInputDf[1:7], caption = "Transcriptomics data")
## ---- echo=TRUE, results='asis'------------------------------------------
clusteredSmallMolecules <- ONION::clusterUsingOntology(
chebiIdsDataFrame = lipidomicsInputDf,
rootColumnName = "ChEBI",
ontologyRepresentatnion = ONION::firstExistsInReactomeChebiOntology)
## ---- echo=FALSE, results='asis'-----------------------------------------
knitr::kable(head(clusteredSmallMolecules, 6))
## ---- echo=TRUE, results='asis'------------------------------------------
mergedSmallMolecules <- ONION::mergeChEBIOntologyWithChildFavoring(
clusteredSmallMolecules,
rootColumnName = 'root')
## ---- echo=FALSE, results='asis'-----------------------------------------
knitr::kable(head(mergedSmallMolecules, 6))
## ---- echo=FALSE, results='asis'-----------------------------------------
knitr::kable(data.frame(
mergedSmallMolecules[1:4, c("ontologyId"), drop = FALSE],
XYZ = c("1","2","3","4"))
)
## ---- echo=TRUE, results='hide'------------------------------------------
chebiIdsToReactomePathways <- ONION::mapReactomePathwaysUnderOrganism(
chebiOntologyIds = mergedSmallMolecules[, c("ontologyId"), drop = FALSE],
organismTaxonomyId = '9606',
idsColumnName = "ontologyId",
rootColumnName = NULL)
chebiIdsToReactomePathwaysWithRoot <- ONION::mapReactomePathwaysUnderOrganism(
chebiOntologyIds = mergedSmallMolecules[, c("ontologyId", "root"), drop = FALSE],
organismTaxonomyId = '9606',
idsColumnName = "ontologyId",
rootColumnName = "root")
## ---- echo=FALSE, results='asis'-----------------------------------------
oneRowDf <- chebiIdsToReactomePathways[6,]
rownames(oneRowDf) <- NULL
knitr::kable(oneRowDf)
## ---- echo=TRUE, results='hide'------------------------------------------
chebiIdsToReactomePathwaysAndToStringNeighbours <- ONION::getStringNeighbours(
chebiIdsToReactomePathways[chebiIdsToReactomePathways$ontologyId == "CHEBI:15756",],
stringOrganismId = 9606,
stringDbVersion = "10",
idsColumnName = 'ontologyId',
rootColumnName = NULL,
listOfEnsembleIdColumnName = 'ensembleIds')
## ---- echo=FALSE, results='asis'-----------------------------------------
chebiIdsToReactomePathwaysAndToStringNeighbours[chebiIdsToReactomePathwaysAndToStringNeighbours$ontologyId == "CHEBI:15756",]$stringIds[[1]] <- chebiIdsToReactomePathwaysAndToStringNeighbours[chebiIdsToReactomePathwaysAndToStringNeighbours$ontologyId == "CHEBI:15756",]$stringIds[[1]][1:50]
chebiIdsToReactomePathwaysAndToStringNeighbours[chebiIdsToReactomePathwaysAndToStringNeighbours$ontologyId == "CHEBI:15756",]$stringGenesSymbols[[1]] <-
chebiIdsToReactomePathwaysAndToStringNeighbours[chebiIdsToReactomePathwaysAndToStringNeighbours$ontologyId == "CHEBI:15756",]$stringGenesSymbols[[1]][1:45]
chebiIdsToReactomePathwaysAndToStringNeighbours[chebiIdsToReactomePathwaysAndToStringNeighbours$ontologyId == "CHEBI:15756",]$ensembleIds[[1]] <-
chebiIdsToReactomePathwaysAndToStringNeighbours[chebiIdsToReactomePathwaysAndToStringNeighbours$ontologyId == "CHEBI:15756",]$ensembleIds[[1]][1:11]
knitr::kable(
chebiIdsToReactomePathwaysAndToStringNeighbours[
chebiIdsToReactomePathwaysAndToStringNeighbours$ontologyId == "CHEBI:15756",]
)
## ---- echo=TRUE, results='asis'------------------------------------------
gmtGroupsFilePath <- paste(find.package("ONION"),"/example/nm-groups.txt", sep = "")
groups <- ONION::readGroupsAsDf(pathToFileWithGroupDefinition = gmtGroupsFilePath)
## ---- echo=FALSE, results='asis'-----------------------------------------
knitr::kable(groups)
## ---- echo=TRUE, results='asis'------------------------------------------
#select small molecules
lip1 <- mergedSmallMolecules[mergedSmallMolecules$root == "CHEBI:27432",]$root
lip2 <- mergedSmallMolecules[mergedSmallMolecules$root == "CHEBI:73705",]$root
joinLip <- c(as.character(lip1), as.character(lip2))
#use Reactome genes mapped to selected small molecules
reactomeTrans1 <- chebiIdsToReactomePathways[chebiIdsToReactomePathways$ontologyId == "CHEBI:15756",]$genesSymbolsFromEnsemble[[1]]
reactomeTrans2 <- chebiIdsToReactomePathways[chebiIdsToReactomePathways$ontologyId == "CHEBI:16015",]$genesSymbolsFromEnsemble[[1]]
joinRecatomeTrans <- c(reactomeTrans1, reactomeTrans2)[!duplicated(c(reactomeTrans1, reactomeTrans2))]
## ---- echo=TRUE, results='asis'------------------------------------------
functionalInteractions <- ONION::createFunctionalInteractionsDataFrame(chebiIdsToReactomePathways)
## ---- echo=FALSE, results='asis'-----------------------------------------
knitr::kable(head(functionalInteractions, 6))
## ---- echo=TRUE, results='asis'------------------------------------------
pathToExampleFileWithXData <- paste(find.package("ONION"),"/example/nm-transcriptomics.txt", sep = "")
pathToExampleFileWithYData <- paste(find.package("ONION"),"/example/nm-lipidomics.txt", sep = "")
XDF <- read.table(pathToExampleFileWithXData, header = TRUE);
YDF <- read.table(pathToExampleFileWithYData, header = TRUE);
ccaResults1 <- ONION::makeCanonicalCorrelationAnalysis(
xNamesVector = joinRecatomeTrans,
yNamesVector = joinLip,
XDataFrame = XDF,
YDataFrame = YDF)
## ---- fig.show='hold', fig.width=6, fig.height=6-------------------------
ONION::plotCanonicalCorrelationAnalysisResults(ccaResults = ccaResults1)
## ---- echo=TRUE, results='hide'------------------------------------------
mccReactome <- ONION::makeCCAOnGroups(
groupsDefinitionDF = groups,
mappingDF = chebiIdsToReactomePathwaysWithRoot,
groupsDataDF = YDF,
mappingDataDF = XDF)
## ---- echo=FALSE, results='hide'-----------------------------------------
permutationTestsResults <- ONION::makePermutationTestOnCCA(
XDataFrame = XDF,
YDataFrame = YDF, 17, 2, 50,
countedCCA = ccaResults1)
## ---- echo=FALSE, results='hide'-----------------------------------------
mccReactome$Molecules[1]
mccReactome$right[[1]]
mccReactome$left[[1]]
mccReactome$ccaResults[[1]]
mccReactome$ccaPermutationTestResults[[1]]
## ---- fig.show='hold', fig.width=6, fig.height=6-------------------------
ONION::plotCanonicalCorrelationAnalysisResults(ccaResults = mccReactome$ccaResults[[1]])
## ---- echo=FALSE, results='hide'-----------------------------------------
PLSResult1 <- ONION::makePartialLeastSquaresRegression(
joinRecatomeTrans,
joinLip,
XDataFrame = XDF,
YDataFrame = YDF)
## ---- fig.show='hold', fig.width=6, fig.height=6-------------------------
ONION::plotRmsepForPLS(PLSResult1$training)
## ---- fig.show='hold', fig.width=6, fig.height=6-------------------------
ONION::plotRegression(PLSResult1$training, ncompValue = 10)
## ---- echo=TRUE, results='asis'------------------------------------------
groupPlsReactome <- ONION::makePLSOnGroups(
groupsDefinitionDF = groups,
mappingDF = chebiIdsToReactomePathwaysWithRoot,
groupsDataDF = YDF,
mappingDataDF = XDF)
## ---- echo=FALSE, results='hide'-----------------------------------------
groupPlsReactome$Molecules[1]
groupPlsReactome$right[[1]]
groupPlsReactome$left[[1]]
groupPlsReactome$plsResults[[1]]
groupPlsReactome$plsPermutationTestResults[[1]]
## ---- fig.show='hold', fig.width=6, fig.height=6, echo=TRUE--------------
ONION::plotRmsepForPLS(groupPlsReactome$plsResults[[1]]$training)
## ---- fig.show='hold', fig.width=6, fig.height=6, echo=TRUE--------------
ONION::plotRegression(groupPlsReactome$plsResults[[1]]$training, ncompValue = 10)
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