Add download for GMT

mlebeur · Jan 2, 2019 · 201e728 · 201e728
1 parent 0ac237e
commit 201e728
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/R/createReport.R b/R/createReport.R
@@ -15,7 +15,7 @@ createReport <- function(hostName, outputDirectory, organism="hsapiens", project
 	dagJson <- list()
 	if(organism!="others"){
 		#####Summary Tab########
-		bodyContent <- summaryDescription(projectName, organism, interestGeneFile, interestGene, interestGeneType, enrichMethod, enrichDatabase, enrichDatabaseFile, enrichDatabaseType, enrichDatabaseDescriptionFile, interestingGeneMap, referenceGeneList, referenceGeneFile, referenceGene, referenceGeneType, referenceSet, minNum, maxNum, sigMethod, fdrThr, topThr, fdrMethod, enrichedSig, dNum, perNum, geneSet)
+		bodyContent <- summaryDescription(projectName, organism, interestGeneFile, interestGene, interestGeneType, enrichMethod, enrichDatabase, enrichDatabaseFile, enrichDatabaseType, enrichDatabaseDescriptionFile, interestingGeneMap, referenceGeneList, referenceGeneFile, referenceGene, referenceGeneType, referenceSet, minNum, maxNum, sigMethod, fdrThr, topThr, fdrMethod, enrichedSig, dNum, perNum, geneSet, hostName)
 
 		if (!is.null(enrichedSig) && dNum < nrow(enrichedSig)) {
 			if (enrichMethod == "ORA") {

diff --git a/R/summaryDescription.R b/R/summaryDescription.R
@@ -1,4 +1,4 @@
-summaryDescription <- function(projectName, organism, interestGeneFile, interestGene, interestGeneType, enrichMethod, enrichDatabase, enrichDatabaseFile, enrichDatabaseType, enrichDatabaseDescriptionFile, interestingGeneMap, referenceGeneList, referenceGeneFile, referenceGene, referenceGeneType, referenceSet, minNum, maxNum, sigMethod, fdrThr, topThr, fdrMethod, enrichedSig, dNum, perNum, geneSet) {
+summaryDescription <- function(projectName, organism, interestGeneFile, interestGene, interestGeneType, enrichMethod, enrichDatabase, enrichDatabaseFile, enrichDatabaseType, enrichDatabaseDescriptionFile, interestingGeneMap, referenceGeneList, referenceGeneFile, referenceGene, referenceGeneType, referenceSet, minNum, maxNum, sigMethod, fdrThr, topThr, fdrMethod, enrichedSig, dNum, perNum, geneSet, hostName) {
 	if(enrichMethod=="ORA"){
 		methodSpecificContent <- specificParameterSummaryOra(organism,referenceGeneList,geneSet,referenceGeneFile,referenceGene,referenceGeneType,referenceSet,minNum,maxNum,sigMethod,fdrThr,topThr,fdrMethod,enrichedSig,dNum,interestingGeneMap)
 	}
@@ -18,7 +18,7 @@ summaryDescription <- function(projectName, organism, interestGeneFile, interest
 			numUserId=nrow(interestingGeneMap$mapped)+length(interestingGeneMap$unmapped),
 			numMappedUserId=nrow(interestingGeneMap$mapped), numUniqueMappedId=length(unique(interestingGeneMap$mapped[[standardId]])),
 			numUnmappedUserId=length(interestingGeneMap$unmapped), idIsEntrezGene=standardId=="entrezgene", standardId=standardId,
-			methodSpecificContent=methodSpecificContent
+			methodSpecificContent=methodSpecificContent, hostName=hostName
 		)
 	}else {
 		data <- list(projectName=projectName, enrichMethod=enrichMethod, organism=organism, organismIsOthers=TRUE,

diff --git a/inst/templates/summary.mustache b/inst/templates/summary.mustache
@@ -30,6 +30,9 @@
 			{{/enrichDatabaseIsOthers}}
 			{{^enrichDatabaseIsOthers}}
 			<b>Enrichment Categories: </b>{{enrichDatabase}}
+			<a class="has-text-info" href="{{hostName}}/api/geneset?organism={{organism}}&database={{enrichDatabase}}&fileType=gmt">
+				<b-icon icon="download" size="is-small"></b-icon>
+			</a>
 			{{/enrichDatabaseIsOthers}}
 		{{/organismIsOthers}}
 		</li>