Nothing
# Subtype
observeEvent(input$tcgaSubtypeBt, {
updateCollapse(session, "collapseTCGASubtype", open = "Subtype data: results")
output$tcgaSubtypetbl <- DT::renderDataTable({
tbl <- subtype.result()
tumor <- isolate({input$tcgasubtypeFilter})
if(!is.null(tbl)) {
closeAlert(session, "tcgaSubtypeAlert")
doi <- c("acc"="Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma<br>doi:10.1016/j.ccell.2016.04.002",
"aml"="Genomic and epigenomic landscapes of adult de novo acute<br>doi:10.1056/NEJMoa1301689",
"blca"="Comprehensive molecular characterization of urothelial bladder <br>doi:10.1038/nature12965",
"brca"="Comprehensive molecular portraits of human breast tumours<br>doi:10.1038/nature11412",
"coad"="Comprehensive molecular characterization of human colon<br>doi:10.1038/nature11252",
"gbm"="Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.<br>doi:10.1016/j.cell.2015.12.028",
"lgg"="Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.<br>doi:10.1016/j.cell.2015.12.028",
"hnsc"="Comprehensive genomic characterization of head and neck<br>doi:10.1038/nature14129",
"kich"="The somatic genomic landscape of chromophobe renal cell carcinoma<br>doi:10.1016/j.ccr.2014.07.014",
"kirc"="Comprehensive molecular characterization of clear cell renal cell carcinoma<br>doi:10.1038/nature12222",
"kirp"="Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma<br>doi:10.1056/NEJMoa1505917",
"lihc"="",
"luad"="Comprehensive molecular profiling of lung adenocarcinoma <br>doi:10.1038/nature13385",
"lusc"="Comprehensive genomic characterization of squamous cell lung cancers<br>doi:10.1038/nature11404",
"ovca"= "Integrated genomic analyses of ovarian carcinoma<br>doi:10.1038/nature10166",
"pancan"="Multiplatform analysis of 12 cancer types reveals molecular <br>doi:10.1016/j.cell.2014.06.049",
"pcpg"="Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma<br>http://dx.doi.org/10.1016/j.ccell.2017.01.001",
"prad"="The Molecular Taxonomy of Primary Prostate Cancer<br>doi:10.1016/j.cell.2015.10.025",
"skcm"="Genomic Classification of Cutaneous Melanoma<br>doi:10.1016/j.cell.2015.05.044",
"stad"="Comprehensive molecular characterization of gastric adenocarcinoma<br>doi:10.1038/nature13480",
"thca"="Integrated genomic characterization of papillary thyroid carcinoma<br>doi:10.1016/j.cell.2014.09.050",
"ucec"="Integrated genomic characterization of endometrial carcinoma<br>doi:10.1038/nature12113",
"ucs"="")
if (isolate({input$saveSubtypeRda}) || isolate({input$saveSubtypeCsv})) {
save.message <- ""
getPath <- parseDirPath(get.volumes(isolate({input$workingDir})), input$workingDir)
if (length(getPath) == 0) getPath <- paste0(Sys.getenv("HOME"),"/TCGAbiolinksGUI")
filename <- file.path(getPath,paste0(tumor,"_subtype.rda"))
if (isolate({input$saveSubtypeRda})) {
save(tbl, file = filename)
save.message <- paste0(save.message,"<br> File created: ", filename)
}
if (isolate({input$saveSubtypeCsv})) {
write_csv(tbl, path = gsub("rda","csv",filename))
save.message <- paste0(save.message,"<br> File created: ", gsub("rda","csv",filename))
}
createAlert(session, "tcgaSubtypemessage", "tcgaSubtypeAlert", title = paste0("Success"), style = "success",
content = paste0(save.message,"<br>Source of the data: ", doi[tumor]), append = TRUE)
} else {
createAlert(session, "tcgaSubtypemessage", "tcgaSubtypeAlert", title = "Source of the data", style = "success",
content = paste0(doi[tumor]), append = TRUE)
}
createTable(tbl)
}
})
})
subtype.result <- reactive({
tumor <- input$tcgasubtypeFilter
tbl <- data.frame()
result = tryCatch({
tbl <- rbind(tbl, TCGAquery_subtype(tumor = tumor))
}, error = function(e) {
createAlert(session, "tcgaSubtypemessage", "tcgaSubtypeAlert", title = "No results found", style = "warning",
content = "Sorry there are subtypes for your query.", append = FALSE)
})
if(is.null(tbl)){
createAlert(session, "tcgaSubtypemessage", "tcgaSubtypeAlert", title = "No results found", style = "warning",
content = "Sorry there are subtypes for your query.", append = FALSE)
return()
} else if(nrow(tbl) ==0) {
createAlert(session, "tcgaSubtypemessage", "tcgaSubtypeAlert", title = "No results found", style = "warning",
content = "Sorry there are subtypes for your query.", append = FALSE)
return()
}
return(tbl)
})
observeEvent(input$subtypePlotCol, {
col <- isolate({input$subtypePlotCol})
if(!is.null(col) & str_length(col) > 1) {
updateCollapse(session, "collapseTCGASubtype", open = "Subtype data: Summary")
}
output$subtypeview <- renderPlotly({
tbl <- subtype.result()
if(is.null(tbl)) return(plotly_empty())
if(is.null(col)) return(plotly_empty())
if(str_length(col) < 2) return(plotly_empty())
df <- as.data.frame(dplyr::count_(tbl, eval(col)))
colnames(df) <- c("Var1","Freq")
df$Var1 <- as.character(df$Var1)
df$Var1[is.na(df$Var1)] <- "No value"
save(df,file = "test.rda")
p <- plot_ly(df, labels = ~Var1, values = ~Freq, type = 'pie',
textposition = 'inside',
textinfo = 'label+percent',
insidetextfont = list(color = '#FFFFFF'),
hoverinfo = 'text',
text=~paste0(Var1,"\n",Freq),
marker = list(colors = colors,
line = list(color = '#FFFFFF', width = 1)),
showlegend = FALSE) %>%
layout(xaxis = list(showgrid = FALSE, zeroline = FALSE, showticklabels = FALSE),
yaxis = list(showgrid = FALSE, zeroline = FALSE, showticklabels = FALSE)) %>%
config(displayModeBar = F)
})
})
observe({
updateSelectizeInput(session, 'subtypePlotCol', choices = colnames(subtype.result()), server = TRUE)
})
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