diff --git a/pvactools/tools/pvacview/server.R b/pvactools/tools/pvacview/server.R index a94556b1..24247f5a 100644 --- a/pvactools/tools/pvacview/server.R +++ b/pvactools/tools/pvacview/server.R @@ -154,7 +154,7 @@ server <- shinyServer(function(input, output, session) { observeEvent(input$loadDefaultmain, { ## Class I demo aggregate report session$sendCustomMessage("unbind-DT", "mainTable") - data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/4ab3139a92d314da7b207e009fd8a1e4715a8166/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_I.all_epitopes.aggregated.tsv") + data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/0359d15c/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_I.all_epitopes.aggregated.tsv") mainData <- read.table(text = data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) colnames(mainData) <- mainData[1, ] mainData <- mainData[-1, ] @@ -167,7 +167,7 @@ server <- shinyServer(function(input, output, session) { mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA" df$mainTable <- mainData ## Class I demo metrics file - metricsdata <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/4ab3139a92d314da7b207e009fd8a1e4715a8166/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_I.all_epitopes.aggregated.metrics.json") + metricsdata <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/0359d15c/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_I.all_epitopes.aggregated.metrics.json") df$metricsData <- fromJSON(txt = metricsdata) df$binding_threshold <- df$metricsData$`binding_threshold` df$allele_specific_binding_thresholds <- df$metricsData$`allele_specific_binding_thresholds` @@ -209,14 +209,14 @@ server <- shinyServer(function(input, output, session) { } rownames(df$comments) <- df$mainTable$ID ## Class II additional demo aggregate report - add_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/4ab3139a92d314da7b207e009fd8a1e4715a8166/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_II.all_epitopes.aggregated.tsv") + add_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/0359d15c/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_II.all_epitopes.aggregated.tsv") addData <- read.table(text = add_data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) colnames(addData) <- addData[1, ] addData <- addData[-1, ] row.names(addData) <- NULL df$additionalData <- addData ## Hotspot gene list autoload - gene_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/4ab3139a92d314da7b207e009fd8a1e4715a8166/pvactools/tools/pvacview/data/cancer_census_hotspot_gene_list.tsv") + gene_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/0359d15c/pvactools/tools/pvacview/data/cancer_census_hotspot_gene_list.tsv") gene_list <- read.table(text = gene_data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) df$gene_list <- gene_list df$mainTable$`Gene of Interest` <- apply(df$mainTable, 1, function(x) {any(x["Gene"] == df$gene_list)})