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server.R
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server.R
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# options(shiny.maxRequestSize = 200*1024^2)
shinyServer(function(input, output, session) {
# Home
observeEvent(input$Browse_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>Invertebrate metazoa</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$metazoa_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>Invertebrate metazoa</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$plant_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>Plant</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$vertebrate_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>Vertebrate</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$SearchByReg_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>Search by genomic location</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$SearchByLIRID_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>Search by LIR identifier</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$BLAST_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>BLAST</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$Annotate_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:18px'>Annotate</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$Quantify_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>Quantify</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$DESeq_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:17px'>DESeq</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$Target_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:18px'>Target</strong>"))
}, ignoreInit = TRUE)
observeEvent(input$Visualize_butt, {
updateNavbarPage(session, "The_page", selected = HTML("<strong style='font-size:18px'>Visualize</strong>"))
}, ignoreInit = TRUE)
# Browse Metazoa
HTML.tab_Metazoa <- read.table("icon.tab_Metazoa.txt", head=F, as.is=T, fill=NA, sep="\t")
colnames(HTML.tab_Metazoa) <- rep("", 8)
output$HTMLtable_Metazoa <- DT::renderDataTable(HTML.tab_Metazoa,
options = list(pageLength = 10, scrollX = TRUE, lengthMenu = c(5, 10, 20, 30, 50, 55),
searchHighlight = TRUE, autoWidth = FALSE, bSort=FALSE),
escape = FALSE, selection=list(mode="single", target="cell"),
rownames= FALSE
)
observe({
if(length(input$HTMLtable_Metazoa_cells_selected) > 0) {
HTML.index <- input$HTMLtable_Metazoa_cells_selected
HTML.index[, 2] <- HTML.index[, 2] + 1
if(!is.na(HTML.tab_Metazoa[HTML.index]) && HTML.tab_Metazoa[HTML.index] != "") {
updateTabsetPanel(session, 'browser_Metazoa', selected = HTML("<strong style='font-size:18px'>LIRs of Invertebrate metazoa</strong>"))
dat.file.path_Metazoa <<- gsub("\\sheight.+", "", HTML.tab_Metazoa[HTML.index])
dat.file.path_Metazoa <- gsub(".+src=", "", dat.file.path_Metazoa)
dat.file.path_Metazoa <- gsub("Icon", "Table", dat.file.path_Metazoa)
dat.file.path_Metazoa <- gsub("png", "dat.gz", dat.file.path_Metazoa)
dat.file.path_Metazoa <- paste0("www/", dat.file.path_Metazoa)
HTML.file.path_Metazoa <<- dat.file.path_Metazoa
dat.content_Metazoa <<- data.table::fread(dat.file.path_Metazoa, data.table = F)
dat.spark.path_Metazoa <- gsub("Table", "Spark_data", dat.file.path_Metazoa)
dat.spark.path_Metazoa <- gsub("dat.gz", "RData", dat.spark.path_Metazoa)
load(dat.spark.path_Metazoa)
dat.spark.target$AN <- NULL
output$LIR_info_num_Metazoa <- DT::renderDataTable(
dat.spark.target,
options = list(
scrollX = TRUE, searching = FALSE, autoWidth = FALSE, bSort=FALSE,
drawCallback = htmlwidgets::JS('function(){debugger;HTMLWidgets.staticRender();}'),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), escape = FALSE, rownames= FALSE, selection="none"
)
output$IRFbrowse_title_Metazoa <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>List of all the LIRs identified by IRF (Click on a row to check the details of the selected LIR):</b></font>')
)
output$IRFbrowse_Metazoa <- DT::renderDT({
DT::datatable(
dat.content_Metazoa, extensions = 'Buttons',
options = list(pageLength = 5, autoWidth = FALSE, lengthMenu = c(5, 10, 20, 30, 50, 100),
searchHighlight = TRUE, scrollX = TRUE,
buttons = list('pageLength', 'copy',
list(extend = 'csv', filename = paste("LIRs", gsub(".dat.gz$", "", basename(dat.file.path_Metazoa)), sep = "_")),
list(extend = 'excel', filename = paste("LIRs", gsub(".dat.gz$", "", basename(dat.file.path_Metazoa)), sep = "_"))
),
dom = 'Bfrtip',
columnDefs=list(list(targets="_all")),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), rownames= FALSE, filter = 'top', selection="single"
)
}, server = TRUE)
} else {
NULL
}
} else {
output$LIR_info_num_Metazoa <- DT::renderDataTable(
NULL
)
output$IRFbrowse_title_Metazoa <- renderText(
NULL
)
output$IRFbrowse_Metazoa <- DT::renderDataTable(
NULL
)
}
})
observe({
if (length(input$IRFbrowse_Metazoa_rows_selected) > 0) {
IRF.index <- input$IRFbrowse_Metazoa_rows_selected
if (!is.na(dat.content_Metazoa$ID[IRF.index])) {
HTML.file.path_Metazoa <- gsub("Table", "HTML", HTML.file.path_Metazoa)
HTML.file.path_Metazoa <- gsub("dat.gz", "IRFresult.RData", HTML.file.path_Metazoa)
load(HTML.file.path_Metazoa)
LIR.gene.op.file.path_Metazoa <- gsub("IRFresult.RData", "LIR_gene_op.txt.gz", HTML.file.path_Metazoa)
LIR.gene.op.file.path_Metazoa <- gsub("HTML", "LIR_gene_op", LIR.gene.op.file.path_Metazoa)
# Overlap between LIRs and genes
output$LIR_gene_op_title_Metazoa <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Overlaps between the selected LIR and genes:</b></font>')
)
output$LIR_gene_op_Metazoa <- DT::renderDT({
if (file.exists(LIR.gene.op.file.path_Metazoa)) {
LIR.gene.op_Metazoa <- data.table::fread(LIR.gene.op.file.path_Metazoa, data.table=F)
LIR.gene.op_Metazoa <- LIR.gene.op_Metazoa[LIR.gene.op_Metazoa$ID %in% dat.content_Metazoa$ID[IRF.index], ]
LIR.gene.op_Metazoa <- LIR.gene.op_Metazoa[, !colnames(LIR.gene.op_Metazoa) %in% c("Match_per", "Indel_per", "Score", "gene.chr")]
} else {
LIR.gene.op_Metazoa <- data.frame("V1"="No data available!")
colnames(LIR.gene.op_Metazoa) <- ""
}
DT::datatable(
LIR.gene.op_Metazoa,
options = list(paging = FALSE, searching = FALSE, autoWidth = FALSE, bSort=FALSE, scrollX = TRUE,
buttons = list('copy',
list(extend = 'csv', filename = "LIR_gene_overlap_in_Browse_result"),
list(extend = 'excel', filename = "LIR_gene_overlap_in_Browse_result")
),
dom = 'Bfrtip',
columnDefs=list(list(targets="_all")),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), escape = FALSE, rownames= FALSE, selection="none", extensions = "Buttons"
)
}, server = FALSE)
# sequence
fasta.file.path_Metazoa <- gsub("HTML", "Fasta", HTML.file.path_Metazoa)
fasta.file.path_Metazoa <- gsub("IRFresult.RData", "LIR.fa.gz", fasta.file.path_Metazoa)
fasta.content_Metazoa <- Biostrings::readBStringSet(fasta.file.path_Metazoa)
LIR.seq.select.fa <- fasta.content_Metazoa[dat.content_Metazoa$ID[IRF.index]]
tmp.fl <- file.path(tempdir(), "LIR.seq.select.fasta")
Biostrings::writeXStringSet(LIR.seq.select.fa, file = tmp.fl, width=20000)
LIR.seq.select <- readLines(tmp.fl)
output$LIR_sequence_title_Metazoa <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <b>Sequence of the selected LIR (<font size="4" color="blue">left flanking sequence in lower case</font> - <font size="4" color="darkcyan">left arm sequence in upper case</font> - <font size="4" color="lightcoral">loop sequence in lower case</font> - <font size="4" color="darkcyan">right arm sequence in upper case</font> - <font size="4" color="blue">right flanking sequence in lower case</font>):</b>')
)
output$LIR_sequence_Metazoa <- renderText({
fa <- LIR.seq.select.fa
fa.len <- Biostrings::width(fa)
names(fa.len) <- names(fa)
fa.L <- stringr::str_locate_all(as.character(fa), "[ACGT]+")
fa.L.nrow <- sapply(fa.L, nrow)
fa.arm <- do.call(rbind, fa.L)
fa.arm <- data.frame(fa.arm, stringsAsFactors = FALSE)
fa.arm$LIR <- rep(names(fa), fa.L.nrow)
fa.arm$length <- fa.len[fa.arm$LIR]
fa.arm <- fa.arm[, c("LIR", "start", "end", "length")]
names(fa.arm) <- c("LIR", "arm_start", "arm_end", "length")
fa.flank <- fa.arm %>% dplyr::group_by(LIR) %>% dplyr::summarise(flank_start = c(1, max(arm_end) + 1), flank_end = c(min(arm_start) - 1, max(length)))
fa.loop <- fa.arm %>% dplyr::group_by(LIR) %>% dplyr::summarise(loop_start = min(arm_end)+1, loop_end = max(arm_start)-1)
fa.loop <- fa.loop[fa.loop$loop_start <= fa.loop$loop_end, ]
fa.arm.fa <- Biostrings::subseq(fa[rep(1, nrow(fa.arm))], fa.arm$arm_start, fa.arm$arm_end)
fa.flank.fa <- Biostrings::subseq(fa[rep(1, nrow(fa.flank))], fa.flank$flank_start, fa.flank$flank_end)
if (nrow(fa.loop) >0) {
fa.loop.fa <- Biostrings::subseq(fa, fa.loop$loop_start, fa.loop$loop_end)
paste0(">", names(fa), "<br>",
'<p style = "word-wrap: break-word;"><font color="blue"><b>', as.character(fa.flank.fa[1]), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa[1]), "</b></font>",
'<font color="lightcoral"><b>', as.character(fa.loop.fa), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa[2]), "</b></font>",
'<font color="blue"><b>', as.character(fa.flank.fa[2]), "</b></font></p>"
)
} else {
paste0(">", names(fa), "<br>",
'<p style = "word-wrap: break-word;"><font color="blue"><b>', as.character(fa.flank.fa[1]), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa), "</b></font>",
'<font color="blue"><b>', as.character(fa.flank.fa[2]), "</b></font></p>"
)
}
})
# alignment of left against right arm
LIR.align.select <- LIR.align[[dat.content_Metazoa$ID[IRF.index]]]
output$LIR_detail_title_Metazoa <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Alignment of the left and right arms of the selected LIR (* indicates complementary match):</b></font>')
)
output$LIR_detail_Metazoa <- renderText(
LIR.align.select, sep = "\n"
)
} else {
NULL
}
} else {
output$LIR_gene_op_title_Metazoa <- renderText(
NULL
)
output$LIR_gene_op_Metazoa <- DT::renderDataTable(
NULL
)
output$LIR_sequence_title_Metazoa <- renderText(
NULL
)
output$LIR_sequence_Metazoa <- renderText(
NULL
)
output$LIR_detail_title_Metazoa <- renderText(
NULL
)
output$LIR_detail_Metazoa <- renderText(
NULL
)
}
})
# Browse Plant
HTML.tab_Plant <- read.table("icon.tab_Plant.txt", head=F, as.is=T, fill=NA, sep="\t")
colnames(HTML.tab_Plant) <- rep("", 8)
output$HTMLtable_Plant <- DT::renderDataTable(HTML.tab_Plant,
options = list(pageLength = 10, scrollX = TRUE, lengthMenu = c(5, 10, 20, 30, 50, 55),
searchHighlight = TRUE, autoWidth = FALSE, bSort=FALSE),
escape = FALSE, selection=list(mode="single", target="cell"),
rownames= FALSE
)
observe({
if(length(input$HTMLtable_Plant_cells_selected) > 0) {
HTML.index <- input$HTMLtable_Plant_cells_selected
HTML.index[, 2] <- HTML.index[, 2] + 1
if(!is.na(HTML.tab_Plant[HTML.index]) && HTML.tab_Plant[HTML.index] != "") {
updateTabsetPanel(session, 'browser_Plant', selected = HTML("<strong style='font-size:18px'>LIRs of Plant</strong>"))
dat.file.path_Plant <<- gsub("\\sheight.+", "", HTML.tab_Plant[HTML.index])
dat.file.path_Plant <- gsub(".+src=", "", dat.file.path_Plant)
dat.file.path_Plant <- gsub("Icon", "Table", dat.file.path_Plant)
dat.file.path_Plant <- gsub("png", "dat.gz", dat.file.path_Plant)
dat.file.path_Plant <- paste0("www/", dat.file.path_Plant)
HTML.file.path_Plant <<- dat.file.path_Plant
dat.content_Plant <<- data.table::fread(dat.file.path_Plant, data.table = F)
dat.spark.path_Plant <- gsub("Table", "Spark_data", dat.file.path_Plant)
dat.spark.path_Plant <- gsub("dat.gz", "RData", dat.spark.path_Plant)
load(dat.spark.path_Plant)
dat.spark.target$AN <- NULL
output$LIR_info_num_Plant <- DT::renderDataTable(
dat.spark.target,
options = list(
scrollX = TRUE, searching = FALSE, autoWidth = FALSE, bSort=FALSE,
drawCallback = htmlwidgets::JS('function(){debugger;HTMLWidgets.staticRender();}'),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), escape = FALSE, rownames= FALSE, selection="none"
)
output$IRFbrowse_title_Plant <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>List of all the LIRs identified by IRF (Click on a row to check the details of the selected LIR):</b></font>')
)
output$IRFbrowse_Plant <- DT::renderDT({
DT::datatable(
dat.content_Plant, extensions = 'Buttons',
options = list(pageLength = 5, autoWidth = FALSE, lengthMenu = c(5, 10, 20, 30, 50, 100),
searchHighlight = TRUE, scrollX = TRUE,
buttons = list('pageLength', 'copy',
list(extend = 'csv', filename = paste("LIRs", gsub(".dat.gz$", "", basename(dat.file.path_Plant)), sep = "_")),
list(extend = 'excel', filename = paste("LIRs", gsub(".dat.gz$", "", basename(dat.file.path_Plant)), sep = "_"))
),
dom = 'Bfrtip',
columnDefs=list(list(targets="_all")),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), rownames= FALSE, filter = 'top', selection="single"
)
}, server = TRUE)
} else {
NULL
}
} else {
output$LIR_info_num_Plant <- DT::renderDataTable(
NULL
)
output$IRFbrowse_title_Plant <- renderText(
NULL
)
output$IRFbrowse_Plant <- DT::renderDataTable(
NULL
)
}
})
observe({
if (length(input$IRFbrowse_Plant_rows_selected) > 0) {
IRF.index <- input$IRFbrowse_Plant_rows_selected
if (!is.na(dat.content_Plant$ID[IRF.index])) {
HTML.file.path_Plant <- gsub("Table", "HTML", HTML.file.path_Plant)
HTML.file.path_Plant <- gsub("dat.gz", "IRFresult.RData", HTML.file.path_Plant)
load(HTML.file.path_Plant)
LIR.gene.op.file.path_Plant <- gsub("IRFresult.RData", "LIR_gene_op.txt.gz", HTML.file.path_Plant)
LIR.gene.op.file.path_Plant <- gsub("HTML", "LIR_gene_op", LIR.gene.op.file.path_Plant)
# Overlap between LIRs and genes
output$LIR_gene_op_title_Plant <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Overlaps between the selected LIR and genes:</b></font>')
)
output$LIR_gene_op_Plant <- DT::renderDT({
if (file.exists(LIR.gene.op.file.path_Plant)) {
LIR.gene.op_Plant <- data.table::fread(LIR.gene.op.file.path_Plant, data.table=F)
LIR.gene.op_Plant <- LIR.gene.op_Plant[LIR.gene.op_Plant$ID %in% dat.content_Plant$ID[IRF.index], ]
LIR.gene.op_Plant <- LIR.gene.op_Plant[, !colnames(LIR.gene.op_Plant) %in% c("Match_per", "Indel_per", "Score", "gene.chr")]
} else {
LIR.gene.op_Plant <- data.frame("V1"="No data available!")
colnames(LIR.gene.op_Plant) <- ""
}
DT::datatable(
LIR.gene.op_Plant,
options = list(paging = FALSE, searching = FALSE, autoWidth = FALSE, bSort=FALSE, scrollX = TRUE,
buttons = list('copy',
list(extend = 'csv', filename = "LIR_gene_overlap_in_Browse_result"),
list(extend = 'excel', filename = "LIR_gene_overlap_in_Browse_result")
),
dom = 'Bfrtip',
columnDefs=list(list(targets="_all")),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), escape = FALSE, rownames= FALSE, selection="none", extensions = "Buttons"
)
}, server = FALSE)
# sequence
fasta.file.path_Plant <- gsub("HTML", "Fasta", HTML.file.path_Plant)
fasta.file.path_Plant <- gsub("IRFresult.RData", "LIR.fa.gz", fasta.file.path_Plant)
fasta.content_Plant <- Biostrings::readBStringSet(fasta.file.path_Plant)
LIR.seq.select.fa <- fasta.content_Plant[dat.content_Plant$ID[IRF.index]]
tmp.fl <- file.path(tempdir(), "LIR.seq.select.fasta")
Biostrings::writeXStringSet(LIR.seq.select.fa, file = tmp.fl, width=20000)
LIR.seq.select <- readLines(tmp.fl)
output$LIR_sequence_title_Plant <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <b>Sequence of the selected LIR (<font size="4" color="blue">left flanking sequence in lower case</font> - <font size="4" color="darkcyan">left arm sequence in upper case</font> - <font size="4" color="lightcoral">loop sequence in lower case</font> - <font size="4" color="darkcyan">right arm sequence in upper case</font> - <font size="4" color="blue">right flanking sequence in lower case</font>):</b>')
)
output$LIR_sequence_Plant <- renderText({
fa <- LIR.seq.select.fa
fa.len <- Biostrings::width(fa)
names(fa.len) <- names(fa)
fa.L <- stringr::str_locate_all(as.character(fa), "[ACGT]+")
fa.L.nrow <- sapply(fa.L, nrow)
fa.arm <- do.call(rbind, fa.L)
fa.arm <- data.frame(fa.arm, stringsAsFactors = FALSE)
fa.arm$LIR <- rep(names(fa), fa.L.nrow)
fa.arm$length <- fa.len[fa.arm$LIR]
fa.arm <- fa.arm[, c("LIR", "start", "end", "length")]
names(fa.arm) <- c("LIR", "arm_start", "arm_end", "length")
fa.flank <- fa.arm %>% dplyr::group_by(LIR) %>% dplyr::summarise(flank_start = c(1, max(arm_end) + 1), flank_end = c(min(arm_start) - 1, max(length)))
fa.loop <- fa.arm %>% dplyr::group_by(LIR) %>% dplyr::summarise(loop_start = min(arm_end)+1, loop_end = max(arm_start)-1)
fa.loop <- fa.loop[fa.loop$loop_start < fa.loop$loop_end, ]
fa.arm.fa <- Biostrings::subseq(fa[rep(1, nrow(fa.arm))], fa.arm$arm_start, fa.arm$arm_end)
fa.flank.fa <- Biostrings::subseq(fa[rep(1, nrow(fa.flank))], fa.flank$flank_start, fa.flank$flank_end)
if (nrow(fa.loop) >0) {
fa.loop.fa <- Biostrings::subseq(fa, fa.loop$loop_start, fa.loop$loop_end)
paste0(">", names(fa), "<br>",
'<p style = "word-wrap: break-word;"><font color="blue"><b>', as.character(fa.flank.fa[1]), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa[1]), "</b></font>",
'<font color="lightcoral"><b>', as.character(fa.loop.fa), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa[2]), "</b></font>",
'<font color="blue"><b>', as.character(fa.flank.fa[2]), "</b></font></p>"
)
} else {
paste0(">", names(fa), "<br>",
'<p style = "word-wrap: break-word;"><font color="blue"><b>', as.character(fa.flank.fa[1]), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa), "</b></font>",
'<font color="blue"><b>', as.character(fa.flank.fa[2]), "</b></font></p>"
)
}
})
# alignment of left against right arm
LIR.align.select <- LIR.align[[dat.content_Plant$ID[IRF.index]]]
output$LIR_detail_title_Plant <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Alignment of the left and right arms of the selected LIR (* indicates complementary match):</b></font>')
)
output$LIR_detail_Plant <- renderText(
LIR.align.select, sep = "\n"
)
} else {
NULL
}
} else {
output$LIR_gene_op_title_Plant <- renderText(
NULL
)
output$LIR_gene_op_Plant <- DT::renderDataTable(
NULL
)
output$LIR_sequence_title_Plant <- renderText(
NULL
)
output$LIR_sequence_Plant <- renderText(
NULL
)
output$LIR_detail_title_Plant <- renderText(
NULL
)
output$LIR_detail_Plant <- renderText(
NULL
)
}
})
# Browse Vertebrate
HTML.tab_Vertebrate <- read.table("icon.tab_Vertebrate.txt", head=F, as.is=T, fill=NA, sep="\t")
colnames(HTML.tab_Vertebrate) <- rep("", 8)
output$HTMLtable_Vertebrate <- DT::renderDataTable(HTML.tab_Vertebrate,
options = list(pageLength = 10, scrollX = TRUE, lengthMenu = c(5, 10, 20, 30, 50, 55),
searchHighlight = TRUE, autoWidth = FALSE, bSort=FALSE),
escape = FALSE, selection=list(mode="single", target="cell"),
rownames= FALSE
)
observe({
if(length(input$HTMLtable_Vertebrate_cells_selected) > 0) {
HTML.index <- input$HTMLtable_Vertebrate_cells_selected
HTML.index[, 2] <- HTML.index[, 2] + 1
if(!is.na(HTML.tab_Vertebrate[HTML.index]) && HTML.tab_Vertebrate[HTML.index] != "") {
updateTabsetPanel(session, 'browser_Vertebrate', selected = HTML("<strong style='font-size:18px'>LIRs of Vertebrate</strong>"))
dat.file.path_Vertebrate <<- gsub("\\sheight.+", "", HTML.tab_Vertebrate[HTML.index])
dat.file.path_Vertebrate <- gsub(".+src=", "", dat.file.path_Vertebrate)
dat.file.path_Vertebrate <- gsub("Icon", "Table", dat.file.path_Vertebrate)
dat.file.path_Vertebrate <- gsub("png", "dat.gz", dat.file.path_Vertebrate)
dat.file.path_Vertebrate <- paste0("www/", dat.file.path_Vertebrate)
HTML.file.path_Vertebrate <<- dat.file.path_Vertebrate
dat.content_Vertebrate <<- data.table::fread(dat.file.path_Vertebrate, data.table = F)
dat.spark.path_Vertebrate <- gsub("Table", "Spark_data", dat.file.path_Vertebrate)
dat.spark.path_Vertebrate <- gsub("dat.gz", "RData", dat.spark.path_Vertebrate)
load(dat.spark.path_Vertebrate)
dat.spark.target$AN <- NULL
output$LIR_info_num_Vertebrate <- DT::renderDataTable(
dat.spark.target,
options = list(
scrollX = TRUE, searching = FALSE, autoWidth = FALSE, bSort=FALSE,
drawCallback = htmlwidgets::JS('function(){debugger;HTMLWidgets.staticRender();}'),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), escape = FALSE, rownames= FALSE, selection="none"
)
output$IRFbrowse_title_Vertebrate <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>List of all the LIRs identified by IRF (Click on a row to check the details of the selected LIR):</b></font>')
)
output$IRFbrowse_Vertebrate <- DT::renderDT({
DT::datatable(
dat.content_Vertebrate, extensions = 'Buttons',
options = list(pageLength = 5, autoWidth = FALSE, lengthMenu = c(5, 10, 20, 30, 50, 100),
searchHighlight = TRUE, scrollX = TRUE,
buttons = list('pageLength', 'copy',
list(extend = 'csv', filename = paste("LIRs", gsub(".dat.gz$", "", basename(dat.file.path_Vertebrate)), sep = "_")),
list(extend = 'excel', filename = paste("LIRs", gsub(".dat.gz$", "", basename(dat.file.path_Vertebrate)), sep = "_"))
),
dom = 'Bfrtip',
columnDefs=list(list(targets="_all")),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), rownames= FALSE, filter = 'top', selection="single"
)
}, server = TRUE)
} else {
NULL
}
} else {
output$LIR_info_num_Vertebrate <- DT::renderDataTable(
NULL
)
output$IRFbrowse_title_Vertebrate <- renderText(
NULL
)
output$IRFbrowse_Vertebrate <- DT::renderDataTable(
NULL
)
}
})
observe({
if (length(input$IRFbrowse_Vertebrate_rows_selected) > 0) {
IRF.index <- input$IRFbrowse_Vertebrate_rows_selected
if (!is.na(dat.content_Vertebrate$ID[IRF.index])) {
HTML.file.path_Vertebrate <- gsub("Table", "HTML", HTML.file.path_Vertebrate)
HTML.file.path_Vertebrate <- gsub("dat.gz", "IRFresult.RData", HTML.file.path_Vertebrate)
load(HTML.file.path_Vertebrate)
LIR.gene.op.file.path_Vertebrate <- gsub("IRFresult.RData", "LIR_gene_op.txt.gz", HTML.file.path_Vertebrate)
LIR.gene.op.file.path_Vertebrate <- gsub("HTML", "LIR_gene_op", LIR.gene.op.file.path_Vertebrate)
# Overlap between LIRs and genes
output$LIR_gene_op_title_Vertebrate <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Overlaps between the selected LIR and genes:</b></font>')
)
output$LIR_gene_op_Vertebrate <- DT::renderDT({
if (file.exists(LIR.gene.op.file.path_Vertebrate)) {
LIR.gene.op_Vertebrate <- data.table::fread(LIR.gene.op.file.path_Vertebrate, data.table=F)
LIR.gene.op_Vertebrate <- LIR.gene.op_Vertebrate[LIR.gene.op_Vertebrate$ID %in% dat.content_Vertebrate$ID[IRF.index], ]
LIR.gene.op_Vertebrate <- LIR.gene.op_Vertebrate[, !colnames(LIR.gene.op_Vertebrate) %in% c("Match_per", "Indel_per", "Score", "gene.chr")]
} else {
LIR.gene.op_Vertebrate <- data.frame("V1"="No data available!")
colnames(LIR.gene.op_Vertebrate) <- ""
}
DT::datatable(
LIR.gene.op_Vertebrate,
options = list(paging = FALSE, searching = FALSE, autoWidth = FALSE, bSort=FALSE, scrollX = TRUE,
buttons = list('copy',
list(extend = 'csv', filename = "LIR_gene_overlap_in_Browse_result"),
list(extend = 'excel', filename = "LIR_gene_overlap_in_Browse_result")
),
dom = 'Bfrtip',
columnDefs=list(list(targets="_all")),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), escape = FALSE, rownames= FALSE, selection="none", extensions = "Buttons"
)
}, server = FALSE)
# sequence
fasta.file.path_Vertebrate <- gsub("HTML", "Fasta", HTML.file.path_Vertebrate)
fasta.file.path_Vertebrate <- gsub("IRFresult.RData", "LIR.fa.gz", fasta.file.path_Vertebrate)
fasta.content_Vertebrate <- Biostrings::readBStringSet(fasta.file.path_Vertebrate)
LIR.seq.select.fa <- fasta.content_Vertebrate[dat.content_Vertebrate$ID[IRF.index]]
tmp.fl <- file.path(tempdir(), "LIR.seq.select.fasta")
Biostrings::writeXStringSet(LIR.seq.select.fa, file = tmp.fl, width=20000)
LIR.seq.select <- readLines(tmp.fl)
output$LIR_sequence_title_Vertebrate <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <b>Sequence of the selected LIR (<font size="4" color="blue">left flanking sequence in lower case</font> - <font size="4" color="darkcyan">left arm sequence in upper case</font> - <font size="4" color="lightcoral">loop sequence in lower case</font> - <font size="4" color="darkcyan">right arm sequence in upper case</font> - <font size="4" color="blue">right flanking sequence in lower case</font>):</b>')
)
output$LIR_sequence_Vertebrate <- renderText({
fa <- LIR.seq.select.fa
fa.len <- Biostrings::width(fa)
names(fa.len) <- names(fa)
fa.L <- stringr::str_locate_all(as.character(fa), "[ACGT]+")
fa.L.nrow <- sapply(fa.L, nrow)
fa.arm <- do.call(rbind, fa.L)
fa.arm <- data.frame(fa.arm, stringsAsFactors = FALSE)
fa.arm$LIR <- rep(names(fa), fa.L.nrow)
fa.arm$length <- fa.len[fa.arm$LIR]
fa.arm <- fa.arm[, c("LIR", "start", "end", "length")]
names(fa.arm) <- c("LIR", "arm_start", "arm_end", "length")
fa.flank <- fa.arm %>% dplyr::group_by(LIR) %>% dplyr::summarise(flank_start = c(1, max(arm_end) + 1), flank_end = c(min(arm_start) - 1, max(length)))
fa.loop <- fa.arm %>% dplyr::group_by(LIR) %>% dplyr::summarise(loop_start = min(arm_end)+1, loop_end = max(arm_start)-1)
fa.loop <- fa.loop[fa.loop$loop_start < fa.loop$loop_end, ]
fa.arm.fa <- Biostrings::subseq(fa[rep(1, nrow(fa.arm))], fa.arm$arm_start, fa.arm$arm_end)
fa.flank.fa <- Biostrings::subseq(fa[rep(1, nrow(fa.flank))], fa.flank$flank_start, fa.flank$flank_end)
if (nrow(fa.loop) >0) {
fa.loop.fa <- Biostrings::subseq(fa, fa.loop$loop_start, fa.loop$loop_end)
paste0(">", names(fa), "<br>",
'<p style = "word-wrap: break-word;"><font color="blue"><b>', as.character(fa.flank.fa[1]), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa[1]), "</b></font>",
'<font color="lightcoral"><b>', as.character(fa.loop.fa), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa[2]), "</b></font>",
'<font color="blue"><b>', as.character(fa.flank.fa[2]), "</b></font></p>"
)
} else {
paste0(">", names(fa), "<br>",
'<p style = "word-wrap: break-word;"><font color="blue"><b>', as.character(fa.flank.fa[1]), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa), "</b></font>",
'<font color="blue"><b>', as.character(fa.flank.fa[2]), "</b></font></p>"
)
}
})
# alignment of left against right arm
LIR.align.select <- LIR.align[[dat.content_Vertebrate$ID[IRF.index]]]
output$LIR_detail_title_Vertebrate <- renderText(
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Alignment of the left and right arms of the selected LIR (* indicates complementary match):</b></font>')
)
output$LIR_detail_Vertebrate <- renderText(
LIR.align.select, sep = "\n"
)
} else {
NULL
}
} else {
output$LIR_gene_op_title_Vertebrate <- renderText(
NULL
)
output$LIR_gene_op_Vertebrate <- DT::renderDataTable(
NULL
)
output$LIR_sequence_title_Vertebrate <- renderText(
NULL
)
output$LIR_sequence_Vertebrate <- renderText(
NULL
)
output$LIR_detail_title_Vertebrate <- renderText(
NULL
)
output$LIR_detail_Vertebrate <- renderText(
NULL
)
}
})
# Search LIR by genomic region
chromosome <- reactive({
req(input$chooseGenomeReg)
if (!exists("genome.info")) {load("genome.info.RData")}
dplyr::filter(genome.info, ID == input$chooseGenomeReg)
})
observeEvent(chromosome(), {
shinyWidgets::updatePickerInput(session, "chooseChromosomeReg", choices = unique(chromosome()$chr))
})
output$searchRegion <- renderUI({
dat.genome <- chromosome()
dat.chromosome <- dat.genome[dat.genome$chr == input$chooseChromosomeReg, ]
if (exists("dat.chromosome") && !is.null(dat.chromosome$size) && nrow(dat.chromosome)>0) {
sliderInput(inputId = "chooseRegion",
label = tags$div(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red">Choose genomic region</font>')),
min = 1, max = dat.chromosome$size,
value = c(1, dat.chromosome$size), width = "100%")
}
})
search.region.result <- eventReactive(input$submitSearchReg, {
dat.file <- paste0(BLASTdb.fl$Division[BLASTdb.fl$Accession == input$chooseGenomeReg], "/", input$chooseGenomeReg, ".dat.gz")
dat.file <- paste0("www/Table/", dat.file)
fasta.file <- paste0(BLASTdb.fl$Division[BLASTdb.fl$Accession == input$chooseGenomeReg], "/", input$chooseGenomeReg, ".LIR.fa.gz")
fasta.file <- paste0("www/Fasta/", fasta.file)
HTML.file <- paste0(BLASTdb.fl$Division[BLASTdb.fl$Accession == input$chooseGenomeReg], "/", input$chooseGenomeReg, ".IRFresult.RData")
HTML.file <- paste0("www/HTML/", HTML.file)
LIR.gene.op.file <- paste0(BLASTdb.fl$Division[BLASTdb.fl$Accession == input$chooseGenomeReg], "/", input$chooseGenomeReg, ".LIR_gene_op.txt.gz")
LIR.gene.op.file <- paste0("www/LIR_gene_op/", LIR.gene.op.file)
if (file.exists(dat.file)) {
dat.search.result <- data.table::fread(dat.file, data.table = FALSE)
dat.search.result <- dat.search.result[dat.search.result$chr == input$chooseChromosomeReg &
dat.search.result$Left_start >= as.numeric(input$chooseRegion[1]) &
dat.search.result$Right_end <= as.numeric(input$chooseRegion[2]), ]
fasta.region <- Biostrings::readBStringSet(fasta.file)
fasta.region <- fasta.region[dat.search.result$ID]
load(HTML.file)
result <- list(dat.search.result, fasta.region, LIR.align, LIR.gene.op.file)
} else {
shinyWidgets::sendSweetAlert(
session = session,
title = "No LIR found!", type = "error",
text = "Please choose a genome to search against."
)
result <- NULL
}
}, ignoreNULL= T)
searchedRegResults <- reactive({
if (is.null(search.region.result())){
} else {
results <- search.region.result()
}
})
output$LIRsearchRegResult <- DT::renderDT({
if (is.null(search.region.result())) {
LIR.search.reg.table <- NULL
} else {
LIR.search.reg.table <- searchedRegResults()[[1]]
}
DT::datatable(
LIR.search.reg.table,
options = list(lengthMenu = c(5, 10, 20, 30, 50), pageLength = 5, searching = TRUE, searchHighlight = TRUE, scrollX = TRUE, autoWidth = FALSE,
buttons = list('pageLength', 'copy',
list(extend = 'csv', filename = "LIRs_in_searched_regions"),
list(extend = 'excel', filename = "LIRs_in_searched_regions")
),
dom = 'Bfrtip',
columnDefs=list(list(targets="_all")),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
), rownames= FALSE, filter = 'top', selection = "single", extensions = "Buttons"
)
}, server = TRUE)
## Download structure of LIRs in user searching result
output$searchRegDownIRFresult.txt <- downloadHandler(
filename <- function() { paste('LIRs_strucutre_search.txt') },
content <- function(file) {
if (is.null(search.region.result())) {
NULL
} else {
write.table(searchedRegResults()[[1]], file, sep="\t", quote=F, row.names = F)
}
}, contentType = 'text/plain'
)
## Download sequence of LIRs in user searching result
output$searchRegDownIRFfasta.txt <- downloadHandler(
filename <- function() { paste('LIRs_sequence_search.fasta') },
content <- function(file) {
if (is.null(search.region.result())) {
NULL
} else {
Biostrings::writeXStringSet(searchedRegResults()[[2]], file)
}
}, contentType = 'text/plain'
)
## Overlap between LIR and genes
output$Search_reg_LIR_gene_op_title <- renderText({
if (is.null(input$LIRsearchRegResult_rows_selected)) {
} else {
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Overlaps between the selected LIR and genes:</b></font>')
}
})
output$Search_reg_LIR_gene_op <- DT::renderDT({
if (is.null(search.region.result()) || is.null(input$LIRsearchRegResult_rows_selected)) {
LIR.gene.op <- NULL
} else {
if (file.exists(searchedRegResults()[[4]])) {
LIR.gene.op <- data.table::fread(searchedRegResults()[[4]], data.table=F)
LIR.ID <- searchedRegResults()[[1]]$ID[input$LIRsearchRegResult_rows_selected]
LIR.gene.op <- LIR.gene.op[LIR.gene.op$ID %in% LIR.ID, ]
LIR.gene.op <- LIR.gene.op[, !colnames(LIR.gene.op) %in% c("Match_per", "Indel_per", "Score", "gene.chr")]
LIR.gene.op
} else {
LIR.gene.op <- data.frame("V1"="No data available!")
colnames(LIR.gene.op) <- ""
}
}
DT::datatable(
LIR.gene.op,
options = list(paging = FALSE, searching = FALSE, autoWidth = FALSE, bSort=FALSE, scrollX = TRUE,
buttons = list('copy',
list(extend = 'csv', filename = "genes_overlap_with_LIR_in_searched_region"),
list(extend = 'excel', filename = "genes_overlap_with_LIR_in_searched_region")
),
dom = 'Bfrtip',
columnDefs=list(list(targets="_all")),
initComplete = DT::JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'background-color': '#000', 'color': '#fff'});",
"}")
),
escape = FALSE, rownames= FALSE, selection="none", extensions = "Buttons"
)
}, server = FALSE)
## Display LIR sequence
output$LIR_detail_search_reg_fasta_title <- renderText({
if (is.null(input$LIRsearchRegResult_rows_selected)) {
} else {
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <b>Sequence of the selected LIR (<font size="4" color="blue">left flanking sequence in lower case</font> - <font size="4" color="darkcyan">left arm sequence in upper case</font> - <font size="4" color="lightcoral">loop sequence in lower case</font> - <font size="4" color="darkcyan">right arm sequence in upper case</font> - <font size="4" color="blue">right flanking sequence in lower case</font>):</b>')
}
})
output$LIR_detail_search_reg_fasta <- renderText({
if (is.null(input$LIRsearchRegResult_rows_selected)) {
} else {
LIR.ID <- searchedRegResults()[[1]]$ID[input$LIRsearchRegResult_rows_selected]
# tmp.fl <- file.path(tempdir(), "t1.fa")
# Biostrings::writeXStringSet(searchedRegResults()[[2]][LIR.ID], file = tmp.fl, width=20000)
# readLines(tmp.fl)
fa <- searchedRegResults()[[2]][LIR.ID]
fa.len <- Biostrings::width(fa)
names(fa.len) <- names(fa)
fa.L <- stringr::str_locate_all(as.character(fa), "[ACGT]+")
fa.L.nrow <- sapply(fa.L, nrow)
fa.arm <- do.call(rbind, fa.L)
fa.arm <- data.frame(fa.arm, stringsAsFactors = FALSE)
fa.arm$LIR <- rep(names(fa), fa.L.nrow)
fa.arm$length <- fa.len[fa.arm$LIR]
fa.arm <- fa.arm[, c("LIR", "start", "end", "length")]
names(fa.arm) <- c("LIR", "arm_start", "arm_end", "length")
fa.flank <- fa.arm %>% dplyr::group_by(LIR) %>% dplyr::summarise(flank_start = c(1, max(arm_end) + 1), flank_end = c(min(arm_start) - 1, max(length)))
fa.loop <- fa.arm %>% dplyr::group_by(LIR) %>% dplyr::summarise(loop_start = min(arm_end)+1, loop_end = max(arm_start)-1)
fa.loop <- fa.loop[fa.loop$loop_start < fa.loop$loop_end, ]
fa.arm.fa <- Biostrings::subseq(fa[rep(1, nrow(fa.arm))], fa.arm$arm_start, fa.arm$arm_end)
fa.flank.fa <- Biostrings::subseq(fa[rep(1, nrow(fa.flank))], fa.flank$flank_start, fa.flank$flank_end)
fa.loop.fa <- Biostrings::subseq(fa, fa.loop$loop_start, fa.loop$loop_end)
paste0(">", LIR.ID, "<br>",
'<p style = "word-wrap: break-word;"><font color="blue"><b>', as.character(fa.flank.fa[1]), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa[1]), "</b></font>",
'<font color="lightcoral"><b>', as.character(fa.loop.fa), "</b></font>",
'<font color="darkcyan"><b>', as.character(fa.arm.fa[2]), "</b></font>",
'<font color="blue"><b>', as.character(fa.flank.fa[2]), "</b></font></p>"
)
}
}, sep = "\n")
## Display LIR alignment
output$LIR_detail_search_reg_title <- renderText({
if (is.null(input$LIRsearchRegResult_rows_selected)) {
} else {
HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Alignment of the left and right arms of the selected LIR (* indicates complementary match):</b></font>')
}
})
output$LIR_detail_search_reg <- renderText({
if (is.null(input$LIRsearchRegResult_rows_selected)) {
} else {
LIR.ID <- searchedRegResults()[[1]]$ID[input$LIRsearchRegResult_rows_selected]
searchedRegResults()[[3]][[LIR.ID]]
}
}, sep = "\n")
# Search by LIR identifier
search.ID.result <- eventReactive(input$submitSearchID, {
if (!is.null(input$chooseGenomeID) && (length(input$chooseGenomeID)>0) && input$chooseGenomeID %in% BLASTdb.fl$Accession) {
dat.file <- paste0(BLASTdb.fl$Division[BLASTdb.fl$Accession == input$chooseGenomeID], "/", input$chooseGenomeID, ".dat.gz")
dat.file <- paste0("www/Table/", dat.file)
fasta.file <- paste0(BLASTdb.fl$Division[BLASTdb.fl$Accession == input$chooseGenomeID], "/", input$chooseGenomeID, ".LIR.fa.gz")
fasta.file <- paste0("www/Fasta/", fasta.file)
HTML.file <- paste0(BLASTdb.fl$Division[BLASTdb.fl$Accession == input$chooseGenomeID], "/", input$chooseGenomeID, ".IRFresult.RData")
HTML.file <- paste0("www/HTML/", HTML.file)
LIR.gene.op.file <- paste0(BLASTdb.fl$Division[BLASTdb.fl$Accession == input$chooseGenomeID], "/", input$chooseGenomeID, ".LIR_gene_op.txt.gz")
LIR.gene.op.file <- paste0("www/LIR_gene_op/", LIR.gene.op.file)
LIR.id <- unlist(strsplit(input$LIRID, split="\\n"))
LIR.id <- gsub("^\\s+", "", LIR.id)
LIR.id <- gsub("\\s+$", "", LIR.id)
if (length(LIR.id) == 0) {
shinyWidgets::sendSweetAlert(
session = session,
title = "No LIR identifier received!", type = "error",
text = "Please input LIR identifier in proper format."
)
result <- NULL
} else {
if (file.exists(dat.file)) {
dat.search.result <- data.table::fread(dat.file, data.table = FALSE)
LIR.id <- intersect(LIR.id, dat.search.result$ID)
if (length(LIR.id)>0) {
dat.search.result <- dat.search.result[dat.search.result$ID %in% LIR.id, ]
fasta.ID <- Biostrings::readBStringSet(fasta.file)
fasta.ID <- fasta.ID[LIR.id]
load(HTML.file)
result <- list(dat.search.result, fasta.ID, LIR.align, LIR.gene.op.file)
} else {
shinyWidgets::sendSweetAlert(
session = session,
title = "Wrong LIR identifiers!", type = "error",
text = "Please check the identifier of all input LIRs!"
)
result <- NULL
}
} else {
result <- NULL
}
}
} else {
shinyWidgets::sendSweetAlert(
session = session,
title = "Please choose a genome to search!", type = "error",
text = ""
)
result <- NULL
}
}, ignoreNULL= T)
searchedIDResults <- reactive({
if (is.null(search.ID.result())){
} else {
results <- search.ID.result()
}
})
# Update Tab Panel
observe({
if (input$submitSearchID >0) {
isolate({
if (!is.null(search.ID.result())) {
updateTabsetPanel(session, 'search_ID', selected = HTML("<strong style='font-size:18px'>Output</strong>"))
} else {
NULL
}
})
} else {NULL}
})
output$LIRsearchIDResult <- DT::renderDT({
if (is.null(search.ID.result())) {