SWApp/server.R at master · StatGenPRD/SWApp · GitHub

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library(shiny)
library(DT)
library(RMySQL)

con <- dbConnect(MySQL(), user="ubuntu", host="localhost", dbname="swapp")
toDisplay <- c("gene", "snp_gwas", "snp_ld", "msh", "pvalue", "gene_score", "gene_rank_min", "evidence", "gene_best", "evidence_best", "pubmed_link")
toDownload <- c("gene", "snp_gwas", "snp_ld", "msh", "pvalue", "gene_score", "gene_rank_min", "evidence", "gene_best", "evidence_best", "pubmedid")

shinyServer(function(input, output) {

				# STOPGAP gene MeSH
				sqlOutput1 <- reactive({

					sqlCode <- paste0("select gene, snp_gwas, snp_ld, msh, pvalue, gene_score, gene_rank_min, evidence, gene_best, evidence_best, pubmedid from swapp.gene_mesh",
									  " where pvalue < ", input$pvalue,
									  " and gene_rank_min >= ", input$gene.rank.min[1], " and gene_rank_min <= ", input$gene.rank.min[2],
									  " and gene_score >= ", input$gene.score[1], " and gene_score <= ", input$gene.score[2],
									  ";")
					sqlOutput <- dbGetQuery(con, sqlCode)
                    sqlOutput$pubmed_link <- paste0("<a href='http://www.ncbi.nlm.nih.gov/pubmed/", sqlOutput$pubmedid, "'>", sqlOutput$pubmedid, "</a>")
                    return(sqlOutput)

				})

				output$table1 <- DT::renderDataTable(sqlOutput1()[toDisplay], server=TRUE, rownames=FALSE, escape=FALSE, filter="top", options=list(pageLength=10))

				output$download1 <- downloadHandler("SWApp.csv", content = function(file) {
										   rows <- input$table1_rows_all
										   write.csv(sqlOutput1()[rows, toDownload], file, quote=TRUE, col.names=TRUE, row.names=FALSE)
				})

				# STOPGAP Best LD
				sqlOutput2 <- reactive({

					sqlCode <- paste0("select gene, snp_gwas, snp_ld, msh, pvalue, gene_score, gene_rank_min, evidence, gene_best, evidence_best, pubmedid from swapp.bestld",
									  " where pvalue < ", input$pvalue,
									  " and gene_rank_min >= ", input$gene.rank.min[1], " and gene_rank_min <= ", input$gene.rank.min[2],
									  " and gene_score >= ", input$gene.score[1], " and gene_score <= ", input$gene.score[2],
									  ";")
					sqlOutput <- dbGetQuery(con, sqlCode)
                    sqlOutput$pubmed_link <- paste0("<a href='http://www.ncbi.nlm.nih.gov/pubmed/", sqlOutput$pubmedid, "'>", sqlOutput$pubmedid, "</a>")
                    return(sqlOutput)

				})

				output$table2 <- DT::renderDataTable(sqlOutput2()[toDisplay], server=TRUE, rownames=FALSE, escape=FALSE, filter="top", options=list(pageLength=10))

				output$download2 <- downloadHandler("SWApp.csv", content = function(file) {
										   rows <- input$table2_rows_all
										   write.csv(sqlOutput2()[rows, toDownload], file, quote=TRUE, col.names=TRUE, row.names=FALSE)
				})


#				# STOPGAP
#				sqlOutput3 <- reactive({
#
#					sqlCode <- paste0("select gene, snp_gwas, snp_ld, msh, pvalue, gene_score, gene_rank_min, evidence, gene_best, evidence_best, pubmedid from swapp",
#									  " where pvalue < ", input$pvalue,
#									  " and gene_rank_min >= ", input$gene.rank.min[1], " and gene_rank_min <= ", input$gene.rank.min[2],
#									  " and gene_score >= ", input$gene.score[1], " and gene_score <= ", input$gene.score[2],
#									  ";")
#					sqlOutput <- dbGetQuery(con, sqlCode)
#                    sqlOutput$pubmed_link <- paste0("<a href='http://www.ncbi.nlm.nih.gov/pubmed/", sqlOutput$pubmedid, "'>", sqlOutput$pubmedid, "</a>")
#                    return(sqlOutput)
#
#				})
#
#				output$table3 <- DT::renderDataTable(sqlOutput3()[toDisplay], server=TRUE, rownames=FALSE, escape=FALSE, filter="top", options=list(pageLength=10))
#
#				output$download3 <- downloadHandler("SWApp.csv", content = function(file) {
#										   rows <- input$table3_rows_all
#										   write.csv(sqlOutput3()[rows, toDownload], file, quote=TRUE, col.names=TRUE, row.names=FALSE)
#				})


})