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+AtSRGA_tutorial_en.pdf filter=lfs diff=lfs merge=lfs -text

AtSRGA_tutorial_en.pdf

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LICENSE.txt

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+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS

data_processing.R

@@ -0,0 +1,176 @@
+## ======================================================== ##
+## Menu : Microarray
+## ======================================================== ##
+
+# Loading data ####
+load("data/microarray/SRscore_microarray.RData")
+colnames_microarray <- colnames(Filter(is.numeric, SRscore_microarray))
+SRscore_microarray[colnames_microarray] <- round(SRscore_microarray[colnames_microarray])
+
+load("data/microarray/SRratio/ABA.RData")
+load("data/microarray/SRratio/cold.RData")
+load("data/microarray/SRratio/DC3000.RData")
+load("data/microarray/SRratio/drought.RData")
+load("data/microarray/SRratio/heat.RData")
+load("data/microarray/SRratio/highlight.RData")
+load("data/microarray/SRratio/hypoxia.RData")
+load("data/microarray/SRratio/osmotic.RData")
+load("data/microarray/SRratio/oxidation.RData")
+load("data/microarray/SRratio/salt.RData")
+load("data/microarray/SRratio/wound.RData")
+
+load("data/microarray/Metadata/ABA.RData")
+load("data/microarray/Metadata/cold.RData")
+load("data/microarray/Metadata/DC3000.RData")
+load("data/microarray/Metadata/drought.RData")
+load("data/microarray/Metadata/heat.RData")
+load("data/microarray/Metadata/highlight.RData")
+load("data/microarray/Metadata/hypoxia.RData")
+load("data/microarray/Metadata/osmotic.RData")
+load("data/microarray/Metadata/oxidation.RData")
+load("data/microarray/Metadata/salt.RData")
+load("data/microarray/Metadata/wound.RData")
+
+# Color settings of a heatmap ####
+paletteLength <- 100
+microarrayBreaks <- c(seq(min(Filter(is.numeric, SRscore_microarray)), 0, length.out = (paletteLength/2)), 
+              seq(0, max(Filter(is.numeric, SRscore_microarray)), length.out = (paletteLength/2))[-1])
+microarrayColor <- colorRampPalette(c("deepskyblue", "white", "hotpink"))(paletteLength)
+
+# Links to external databases ####
+link <- rep("link", nrow(SRscore_microarray))
+
+## AlphaFold2
+url <- rep(paste0("https://alphafold.ebi.ac.uk/search/text/",
+                  SRscore_microarray$ensembl_gene_id))
+AF2 <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## ATTED-II
+url <- rep(paste0("https://atted.jp/kwsearch/?stype=any&kword=", 
+                  SRscore_microarray$ensembl_gene_id, 
+                  "&searchBtnK.x=0&searchBtnK.y=0"))
+ATTED2 <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## eFP Browser
+url <- rep(paste0("https://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=Abiotic_Stress&mode=Absolute&primaryGene=",
+                  SRscore_microarray$ensembl_gene_id))
+eFP <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## KEGG
+url <- rep(paste0("https://www.genome.jp/dbget-bin/www_bget?ath:", SRscore_microarray$ensembl_gene_id))
+KEGG <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## STRING
+url <- rep(paste0("https://string-db.org/cgi/network?identifiers=",
+                  SRscore_microarray$ensembl_gene_id,
+                  "&species=3702&show_query_node_labels=1"))
+STRING <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## TAIR
+url <- rep(paste0("https://www-arabidopsis-org.translate.goog/servlets/TairObject?type=locus&name=", 
+                  SRscore_microarray$ensembl_gene_id, 
+                  "&_x_tr_sl=en&_x_tr_tl=ja&_x_tr_hl=ja&_x_tr_pto=sc"))
+TAIR <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## ThaleMine
+url <- rep(paste0("https://bar.utoronto.ca/thalemine/keywordSearchResults.do?searchTerm=",
+                  SRscore_microarray$ensembl_gene_id, "&searchSubmit=GO"))
+TM <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## Joining links to the atlas
+SRscore_microarray <- cbind(SRscore_microarray, "AlphaFold2" = AF2, "ATTED-II" = ATTED2, "eFP Browser" = eFP, 
+                         "KEGG" = KEGG, "STRING" = STRING, "TAIR" = TAIR, "Thale Mine" = TM)
+
+## Convert the atlas to template matching format 
+genefinder_microarray <- column_to_rownames(SRscore_microarray, var = "ensembl_gene_id")
+genefinder_microarray <- Filter(is.numeric, genefinder_microarray)
+genefinder_microarray <- as.matrix(genefinder_microarray)
+
+
+## ========================================================= ##
+## Menu : RNA-Seq
+## ========================================================= ##
+
+# Loading data ####
+load("data/rnaseq/SRscore_rnaseq.RData")
+colnames_rnaseq <- colnames(Filter(is.numeric, SRscore_rnaseq))
+SRscore_rnaseq[colnames_rnaseq] <- round(SRscore_rnaseq[colnames_rnaseq])
+
+load("data/rnaseq/SRratio/ABA.RData")
+load("data/rnaseq/SRratio/cold.RData")
+load("data/rnaseq/SRratio/DC3000.RData")
+load("data/rnaseq/SRratio/drought.RData")
+load("data/rnaseq/SRratio/heat.RData")
+load("data/rnaseq/SRratio/highlight.RData")
+load("data/rnaseq/SRratio/hypoxia.RData")
+load("data/rnaseq/SRratio/osmotic.RData")
+load("data/rnaseq/SRratio/oxidation.RData")
+load("data/rnaseq/SRratio/salt.RData")
+load("data/rnaseq/SRratio/wound.RData")
+
+load("data/rnaseq/Metadata/ABA.RData")
+load("data/rnaseq/Metadata/cold.RData")
+load("data/rnaseq/Metadata/DC3000.RData")
+load("data/rnaseq/Metadata/drought.RData")
+load("data/rnaseq/Metadata/heat.RData")
+load("data/rnaseq/Metadata/highlight.RData")
+load("data/rnaseq/Metadata/hypoxia.RData")
+load("data/rnaseq/Metadata/osmotic.RData")
+load("data/rnaseq/Metadata/oxidation.RData")
+load("data/rnaseq/Metadata/salt.RData")
+load("data/rnaseq/Metadata/wound.RData")
+
+# Color settings of a heatmap ####
+paletteLength <- 100
+rnaseqBreaks <- c(seq(min(Filter(is.numeric, SRscore_rnaseq)), 0, length.out = (paletteLength/2)), 
+                  seq(0, max(Filter(is.numeric, SRscore_rnaseq)), length.out = (paletteLength/2))[-1])
+rnaseqColor <- colorRampPalette(c("deepskyblue", "white", "hotpink"))(paletteLength)
+
+# Links to external databases ####
+link <- rep("link", nrow(SRscore_rnaseq))
+
+## AlphaFold2
+url <- rep(paste0("https://alphafold.ebi.ac.uk/search/text/",
+                  SRscore_rnaseq$ensembl_gene_id))
+AF2 <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## ATTED-II
+url <- rep(paste0("https://atted.jp/kwsearch/?stype=any&kword=", 
+                  SRscore_rnaseq$ensembl_gene_id, 
+                  "&searchBtnK.x=0&searchBtnK.y=0"))
+ATTED2 <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## eFP Browser
+url <- rep(paste0("https://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=Abiotic_Stress&mode=Absolute&primaryGene=",
+                  SRscore_rnaseq$ensembl_gene_id))
+eFP <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## KEGG
+url <- rep(paste0("https://www.genome.jp/dbget-bin/www_bget?ath:", SRscore_rnaseq$ensembl_gene_id))
+KEGG <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## STRING
+url <- rep(paste0("https://string-db.org/cgi/network?identifiers=",
+                  SRscore_rnaseq$ensembl_gene_id,
+                  "&species=3702&show_query_node_labels=1"))
+STRING <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## TAIR
+url <- rep(paste0("https://www-arabidopsis-org.translate.goog/servlets/TairObject?type=locus&name=", 
+                  SRscore_rnaseq$ensembl_gene_id, 
+                  "&_x_tr_sl=en&_x_tr_tl=ja&_x_tr_hl=ja&_x_tr_pto=sc"))
+TAIR <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+## ThaleMine
+url <- rep(paste0("https://bar.utoronto.ca/thalemine/keywordSearchResults.do?searchTerm=",
+                  SRscore_rnaseq$ensembl_gene_id, "&searchSubmit=GO"))
+TM <- paste0("<a href = ", "'", url, "'", ">", link, "</a>")
+
+# Joining links to the atlas
+SRscore_rnaseq <- cbind(SRscore_rnaseq, "AlphaFold2" = AF2, "ATTED-II" = ATTED2, "eFP Browser" = eFP,
+                     "KEGG" = KEGG, "STRING" = STRING, "TAIR" = TAIR, "Thale Mine" = TM)
+
+# Convert the atlas to template matching format 
+genefinder_rnaseq <- column_to_rownames(SRscore_rnaseq, var = "ensembl_gene_id")
+genefinder_rnaseq <- Filter(is.numeric, genefinder_rnaseq)
+genefinder_rnaseq <- as.matrix(genefinder_rnaseq)

global.R

@@ -0,0 +1,440 @@
+# Source scripts
+# source("proxy.R", local = TRUE)
+source("setup.R", local = TRUE)
+source("data_processing.R", local = TRUE)
+
+
+# Sub Menu : Atlas ####
+## Tab : Overview ####
+overviewUI <- function(id) {
+  ns <- NS(id)
+  tagList(
+    actionButton(ns("reset"), "Reset Table"),
+    actionButton(ns("remove"), "Remove",
+                 style = "color: red"),
+    br(),
+    br(),
+    dataTableOutput(ns("atlas")),
+    br(),
+    br(),
+    sidebarLayout(
+      sidebarPanel(h3(strong("Bulk Search → Heatmap")), width = 3,
+                   textAreaInput(ns("text"), h4("1. Input list of identifiers :"),
+                                 width = "400px", height = "300px"
+                   ),
+                   actionButton(ns("submit"), "Submit",
+                                style = "color: white; background-color: #337ab7; border-color: #2e6da4"),
+                   actionButton(ns("example1"), "Example1"),
+                   actionButton(ns("example2"), "Example2"),
+                   br(),
+                   h4("You can remove inappropriate rows if any."),
+                   "1. Select rows in the table.",
+                   br(),
+                   "2. Click 'Remove' button above the table.",
+                   br(),
+                   br(),
+                   h4("2. Control paremeters of heatmap"),
+                   selectInput(ns("identifier"),
+                               label = "Choose y axis :",
+                               choices = c("ensembl_gene_id",
+                                           "SYMBOL"),
+                               selected = "ensembl_gene_id"),
+                   numericInput(ns("height"),
+                                label = "height :",
+                                value = 400),
+                   actionButton(ns("heatmap"), "Plot",
+                                style = "color: white; background-color: #337ab7; border-color: #2e6da4")
+      ),
+      mainPanel(
+        dataTableOutput(ns("bulk"))
+      )
+    )
+  )
+}
+
+overview <- function(input, output, session, srga, cl, Breaks, Color) {
+  ##　Table Display : SRGA (Stress Response Gene Atlas) ####
+  ### Display the atlas as a heatmap ####
+  rv  <- reactiveValues(df = NULL)
+  rv$df <- srga
+  observeEvent(input$reset, {
+    rv$df <- srga
+  })
+  output$atlas <- renderDataTable({
+    datatable(
+      rv$df,
+      filter = "top",
+      selection = "single",
+      extensions = c("Buttons", "FixedColumns"),
+      escape = FALSE,
+      rownames = FALSE,
+      options = list(columnDefs = list(list(className = "dt-nowrap", targets = "_all"),
+                                       list(visible = FALSE, targets = NULL)),
+                     scrollX = TRUE, 
+                     fixedColumns = TRUE,
+                     dom = "lrtBip",
+                     buttons = list(
+                       I("colvis"),
+                       list(extend = "collection",
+                            buttons = list(list(extend = "csv", filename = "SRGA"),
+                                           list(extend = "excel", filename = "SRGA")
+                            ),
+                            text = "Download"))
+      )
+    ) %>%
+      formatStyle(names(srga[cl]), backgroundColor = styleInterval(Breaks, Color))
+  }, server = TRUE)
+  
+  ## Side Bar : Bulk Search → Heatmap ####
+  ### Input string ####
+  #### Lowercase conversion and delimiter splitting（space or break or tab or commma）####
+  lower_input <- reactive({
+    strsplit(tolower(input$text), " |\n|\t|,")[[1]]
+  })
+  
+  #### Get index of AGI code ####
+  agi_index <- reactive({
+    grepl("at.g.+", lower_input(), ignore.case = T)
+  })
+  
+  #### Delete Version Part of AGI Code（e.g., ATXGXXXX.1, ATXGXXXXX.3） ####
+  key <- reactive({
+    c(gsub("\\..+", "", lower_input()[agi_index()]), lower_input()[!agi_index()])
+  })
+  
+  ### SRGA ####
+  #### Extract AGI code and SYMBOL for each line
+  AGIandSYMBOL <- reactive(apply(srga[c("ensembl_gene_id", "SYMBOL")], 1, paste, collapse = "/"))
+  
+  #### Divide with a slash ####
+  splited_AGIandSYMBOL <- reactive(strsplit(AGIandSYMBOL(), "/"))
+  
+  #### Convert to lowcase ####
+  lowered_AGIandSYMBOL <- reactive(lapply(splited_AGIandSYMBOL(), tolower))
+  
+  #### Get the index of the element that exactly matches the input string ####
+  matched_AGIandSYMBOL <- reactive(lapply(lowered_AGIandSYMBOL(), match, key()[which(key() != "")]))
+  
+  ### Retrieve the row corresponding to the number from SRGA ####
+  observeEvent(input$submit, {
+    rv$df <- srga[which(lapply(matched_AGIandSYMBOL(), any) == TRUE), ]
+  })
+  
+  ### Remove line ####
+  observeEvent(input$remove, {
+    rv$df <- rv$df[-as.numeric(input$atlas_rows_selected), ]
+  })
+  
+  ### Example of input string ####
+  #### First ####
+  observeEvent(input$example1, {
+    name <- paste("ADH1", "DREB1A", "ELIP1", "HSP17.8", "JAZ1", "NCED3", "PP2CA")
+    updateTextAreaInput(session, "text", value = name)
+  })
+  #### Second ####
+  observeEvent(input$example2, {
+    name <- paste("DREB1A", "DREB1B", "DREB1C", "DREB2A", "DREB2B", "GolS1", "GolS2", "GolS3", sep = "\n")
+    updateTextAreaInput(session, "text", value = name)
+  })
+  
+  ### Create a heatmap ####
+  heatmap_tbl <- reactive(
+    heatmaply(Filter(is.numeric,
+                     set_rownames(rv$df, value = rv$df[, input$identifier])),
+              height = input$height,
+              grid_gap = 0.2, grid_color = "gray90",
+              scale_fill_gradient_fun = scale_fill_gradient2(
+                low = "deepskyblue",
+                high = "hotpink",
+                midpoint = 0
+              ),
+              Rowv = FALSE,
+              Colv = FALSE,
+              cellnote = Filter(is.numeric,
+                                set_rownames(rv$df, value = rv$df[, input$identifier])),
+              cellnote_size = 18,
+              cellnote_textposition = "middle center")
+  )
+  
+  ### Display the heatmap inside the modal dialog box ####
+  output$plot <- renderPlotly({
+    heatmap_tbl()
+  })
+  ns <- session$ns
+  observeEvent(input$heatmap, {
+    showModal(modalDialog({
+      plotlyOutput(ns("plot"))},
+      easyClose = TRUE,
+      size = "l",
+      title = "Heatmap"))
+  })
+  
+  return(reactive(rv$df$ensembl_gene_id[input$atlas_rows_selected]))
+}
+
+## Tab : Abiotic and biotic stress ####
+stressUI <- function(id) {
+  ns <- NS(id)
+  tagList(
+    br(),
+    actionButton(ns("button_ratio"), "Show SRratio", icon("table"),
+                 style = "color: white; background-color: #337ab7; border-color: #2e6da4"),
+    br(),
+    br(),
+    dataTableOutput(ns("ratio")),
+    br(),
+    br(),
+    br(),
+    actionButton(ns("button_metadata"), "Show metadata", icon("table"),
+                 style = "color: white; background-color: #337ab7; border-color: #2e6da4"),
+    actionButton(ns("button_metadata_more"), "", icon("filter"),
+                 style = "color: pink; background-color: white; border-color: #2e6da4"),
+    actionButton(ns("button_metadata_middle"), "", icon("filter"),
+                 style = "color: black; background-color: white; border-color: #2e6da4"),
+    actionButton(ns("button_metadata_less"), "", icon("filter"),
+                 style = "color: skyblue; background-color: white; border-color: #2e6da4"),
+    br(),
+    dataTableOutput(ns("metadata"))
+  )
+}
+
+stress <- function(input, output, session, ratio, srga, selectedRow, metadata) {
+  ## Table Display : SRratio ####
+  ### Retrieve the SRratio of the specified gene (改善点あり) ####
+  selectedRatio <- reactive({
+    ratio[which(ratio$ensembl_gene_id %in% selectedRow()), ]
+  })
+  
+  rv <- reactiveValues(ratio = NULL, metadata = NULL)
+  
+  observeEvent(input$button_ratio, {
+    rv$ratio <- ratio[which(ratio$ensembl_gene_id %in% selectedRow()), ]
+  })
+  
+  ### Display SRratio ####
+  output$ratio <- renderDataTable({
+    datatable(rv$ratio,
+              extensions = c("Buttons", "FixedColumns"),
+              rownames = FALSE,
+              selection = "single",
+              options = list(scrollX =TRUE, fixedColumns = TRUE)) %>%
+      formatStyle(colnames(selectedRatio())[-1], backgroundColor = styleInterval(c(-2, 2), c("skyblue", "white", "pink")))
+  })
+  
+  ### Identify the treated samples that meet the following criteria ####
+  #### SRratio ≧ 2 (1) ####
+  more <- reactive({
+    which(metadata$treated_sample %in% colnames(rv$ratio)[rv$ratio >= 2])
+  })
+  
+  #### -2 < SRratio < 2 ####
+  middle <- reactive({
+    which(metadata$treated_sample %in% colnames(rv$ratio)[-2 <= rv$ratio & rv$ratio <= 2])
+  })
+  
+  #### SRratio ≦ -2 (2) ####
+  less <- reactive({
+    which(metadata$treated_sample %in% colnames(rv$ratio)[rv$ratio <= -2])
+  })
+  
+  ## Table Display : Metadata ####
+  ### Color the metadata (1 → pink、2 → skyblue) ####
+  observeEvent(input$button_metadata, {
+    rv$metadata <- datatable(
+      metadata,
+      selection = "single",
+      rownames = FALSE,
+      options = list(paging = FALSE,
+                     scrollY = "1000px",
+                     columnDefs = list(list(className = 'dt-nowrap', targets = "_all")),
+                     dom = 'flrtBip', 
+                     buttons = list(list(extend = 'collection',
+                                         buttons = list(list(extend = 'csv', filename = 'Metadata'),
+                                                        list(extend = 'excel', filename = 'Metadata')),
+                                         text = 'Download')))) %>% 
+      formatStyle(
+        "treated_sample", 
+        target = "row",
+        backgroundColor = styleRow(c(more(), less()), c(rep("pink", length(more())), rep("skyblue", length(less())))
+        )
+      )
+  })
+  
+  ### Retrieve the metadata under the any following conditions  ####
+  #### SRratio ≧ 2 ####
+  observeEvent(input$button_metadata_more, {
+    rv$metadata <- datatable(
+      metadata[more(), ],
+      selection = "single",
+      rownames = FALSE,
+      options = list(columnDefs = list(list(className = 'dt-nowrap', targets = "_all")),
+                     dom = 'flrtBip', 
+                     buttons = list(list(extend = 'collection',
+                                         buttons = list(list(extend = 'csv', filename = 'Metadata_detected_up'),
+                                                        list(extend = 'excel', filename = 'Metadata_detected_up')),
+                                         text = 'Download')))
+    )
+  })
+  
+  #### -2 < SRratio < 2 ####
+  observeEvent(input$button_metadata_middle, {
+    rv$metadata <- datatable(
+      metadata[middle(), ],
+      selection = "single",
+      rownames = FALSE,
+      options = list(columnDefs = list(list(className = 'dt-nowrap', targets = "_all")),
+                     dom = 'flrtBip', 
+                     buttons = list(list(extend = 'collection',
+                                         buttons = list(list(extend = 'csv', filename = 'Metadata_not_detected'),
+                                                        list(extend = 'excel', filename = 'Metadata_not_detected')),
+                                         text = 'Download')))
+    )
+  })
+  
+  #### SRratio ≦ -2 ####
+  observeEvent(input$button_metadata_less, {
+    rv$metadata <- datatable(
+      metadata[less(), ],
+      selection = "single",
+      rownames = FALSE,
+      options = list(columnDefs = list(list(className = 'dt-nowrap', targets = "_all")),
+                     dom = 'flrtBip', 
+                     buttons = list(list(extend = 'collection',
+                                         buttons = list(list(extend = 'csv', filename = 'Metadata_detected_down'),
+                                                        list(extend = 'excel', filename = 'Metadata_detected_down')),
+                                         text = 'Download')))
+    )
+  })
+  
+  ### Display metadata ####
+  output$metadata <- renderDataTable({
+    rv$metadata
+  }, server = FALSE)
+}
+
+
+
+
+# Sub Menu : Template Matching ####
+TemplateMatchUI <- function(id) {
+  ns <- NS(id)
+  
+  tagList(
+    sidebarLayout(
+      sidebarPanel(h3(strong("Teplate Matching → Heatmap")), width = 3,
+                   h4("1. Select a gene in overview"),
+                   selectInput(ns("method"), 
+                               label = "Choose a method :",
+                               choices = c("euclidean","maximum", "manhattan", 
+                                           "canberra", "correlation", "binary"),
+                               selected = "euclidean"),
+                   numericInput(ns("display"),
+                                label = "Number of results to display :",
+                                value = 5),
+                   h4("2. Control paremeters of heatmap"),
+                   selectInput(ns("identifier"),
+                               label = "Choose y axis :",
+                               choices = c("ensembl_gene_id",
+                                           "SYMBOL"),
+                               selected = "ensembl_gene_id"),
+                   numericInput(ns("height"),
+                                label = "height :",
+                                value = 400),
+                   actionButton(ns("heatmap"), "Plot",
+                                style = "color: white; background-color: #337ab7; border-color: #2e6da4")
+      ),
+      mainPanel(width = 9,
+                dataTableOutput(ns("close_genes")),
+                dataTableOutput(ns("selected"))
+      )
+    )
+  )
+}
+
+
+TemplateMatch <- function(input, output, session, query, selectRow, srga, cl, Breaks, Color) {
+  ## Table Display : Template Matching results ####
+  ### Template matching ####
+  close_genes <- reactive({
+    genefinder(query,
+               selectRow(),
+               input$display,
+               method = input$method)})
+  
+  ### Display matching result ####
+  output$close_genes <- renderDataTable({
+    datatable(
+      add_column(srga[close_genes()[[1]]$indices, ], 
+                 "dists" = round(close_genes()[[1]]$dists, digits = 3),
+                 .after = max(which(sapply(srga, is.numeric)))
+      ),
+      filter = "top",
+      selection = "single",
+      extensions = c("Buttons", "FixedColumns"),
+      options = list(columnDefs = list(list(className = 'dt-nowrap', targets = "_all")),
+                     scrollX = TRUE, fixedColumns = TRUE,
+                     dom = 'lrtBip', buttons = list(list(extend = 'collection',
+                                                         buttons = list(list(extend = 'csv', filename = 'closegenes'),
+                                                                        list(extend = 'excel', filename = 'closegenes')),
+                                                         text = 'Download'))
+      ),
+      escape = FALSE, rownames = FALSE
+    ) %>%
+      formatStyle(names(srga[cl]), backgroundColor = styleInterval(Breaks, Color)) %>%
+      formatStyle("dists", backgroundColor = "yellow")
+  },
+  server = FALSE)
+  
+  ### Display template ####
+  output$selected <- renderDataTable({
+    datatable(
+      srga[selectRow(), ],
+      filter = "top",
+      extensions = c("Buttons", "FixedColumns"),
+      selection = "single",
+      options = list(columnDefs = list(list(className = 'dt-nowrap', targets = "_all")),
+                     scrollX = TRUE, 
+                     fixedColumns = TRUE,
+                     dom = 'lrtBip', buttons = list(list(extend = 'collection',
+                                                         buttons = list(list(extend = 'csv', filename = 'template'),
+                                                                        list(extend = 'excel', filename = 'template')),
+                                                         text = 'Download'))
+      ),
+      escape = FALSE, rownames = FALSE
+    ) %>%
+      formatStyle(names(srga[cl]), backgroundColor = styleInterval(Breaks, Color))
+  })
+  
+  output$test <- renderDataTable({})
+  
+  ## Side Bar : Template Matching → Heatmap ####
+  ### Create heatmap ####
+  heatmap_tbl <- reactive(
+    heatmaply(Filter(is.numeric,
+                     set_rownames(srga[close_genes()[[1]]$indices, ], 
+                                  value = srga[close_genes()[[1]]$indices, input$identifier])),
+              height = input$height,
+              grid_gap = 0.2, grid_color = "gray90",
+              scale_fill_gradient_fun = scale_fill_gradient2(
+                low = "deepskyblue",
+                high = "hotpink",
+                midpoint = 0
+              ),
+              Rowv = FALSE,
+              Colv = FALSE)
+  )
+  
+  ### Display a heatmap inside the modal dialog box ####
+  output$plot <- renderPlotly({
+    heatmap_tbl()
+  })
+  ns <- session$ns
+  observeEvent(input$heatmap, {
+    showModal(modalDialog({
+      plotlyOutput(ns("plot"))},
+      easyClose = TRUE,
+      size = "l",
+      title = "Heatmap")
+    )
+  })
+}

server.R

@@ -0,0 +1,47 @@
+shinyServer(function(input, output, session) {
+  ## ======================================================== ##
+  ## Menu : Microarray
+  ## ======================================================== ##
+  ## ======================================== ##
+  ## Sub Menu : Atlas
+  ## ======================================== ##
+  select_microarray <- callModule(overview, "microarray", SRscore_microarray, colnames_microarray, microarrayBreaks, microarrayColor)
+  callModule(stress, "ABAm", ABA_ratiom, SRscore_microarray, select_microarray, ABA_metadatam)
+  callModule(stress, "coldm", cold_ratiom, SRscore_microarray, select_microarray, cold_metadatam)
+  callModule(stress, "DC3000m", DC3000_ratiom, SRscore_microarray, select_microarray, DC3000_metadatam)
+  callModule(stress, "droughtm", drought_ratiom, SRscore_microarray, select_microarray, drought_metadatam)
+  callModule(stress, "heatm", heat_ratiom, SRscore_microarray, select_microarray, heat_metadatam)
+  callModule(stress, "highlightm", highlight_ratiom, SRscore_microarray, select_microarray, highlight_metadatam)
+  callModule(stress, "hypoxiam", hypoxia_ratiom, SRscore_microarray, select_microarray, hypoxia_metadatam)
+  callModule(stress, "osmoticm", osmotic_ratiom, SRscore_microarray, select_microarray, osmotic_metadatam)
+  callModule(stress, "oxidationm", oxidation_ratiom, SRscore_microarray, select_microarray, oxidation_metadatam)
+  callModule(stress, "saltm", salt_ratiom, SRscore_microarray, select_microarray, salt_metadatam)
+  callModule(stress, "woundm", wound_ratiom, SRscore_microarray, select_microarray, wound_metadatam)
+  ## ======================================== ##
+  ## Sub Menu : Template Matching
+  ## ======================================== ##
+  callModule(TemplateMatch, "microarray", genefinder_microarray, select_microarray, SRscore_microarray, colnames_microarray, microarrayBreaks, microarrayColor)
+
+  ## ========================================================= ##
+  ## Menu : RNA-Seq
+  ## ========================================================= ##
+  ## ======================================== ##
+  ## Sub Menu : Atlas
+  ## ======================================== ##
+  select_rnaseq <- callModule(overview, "rnaseq", SRscore_rnaseq, colnames_rnaseq, rnaseqBreaks, rnaseqColor)
+  callModule(stress, "ABAr", ABA_ratior, SRscore_rnaseq, select_rnaseq, ABA_metadatar)
+  callModule(stress, "coldr", cold_ratior, SRscore_rnaseq, select_rnaseq, cold_metadatar)
+  callModule(stress, "DC3000r", DC3000_ratior, SRscore_rnaseq, select_rnaseq, DC3000_metadatar)
+  callModule(stress, "droughtr", drought_ratior, SRscore_rnaseq, select_rnaseq, drought_metadatar)
+  callModule(stress, "heatr", heat_ratior, SRscore_rnaseq, select_rnaseq, heat_metadatar)
+  callModule(stress, "highlightr", highlight_ratior, SRscore_rnaseq, select_rnaseq, highlight_metadatar)
+  callModule(stress, "hypoxiar", hypoxia_ratior, SRscore_rnaseq, select_rnaseq, hypoxia_metadatar)
+  callModule(stress, "osmoticr", osmotic_ratior, SRscore_rnaseq, select_rnaseq, osmotic_metadatar)
+  callModule(stress, "oxidationr", oxidation_ratior, SRscore_rnaseq, select_rnaseq, oxidation_metadatar)
+  callModule(stress, "salt", salt_ratior, SRscore_rnaseq, select_rnaseq, salt_metadatar)
+  callModule(stress, "wound", wound_ratior, SRscore_rnaseq, select_rnaseq, wound_metadatar)
+  ## ======================================== ##
+  ## Sub Menu : Template Matching
+  ## ======================================== ##
+  callModule(TemplateMatch, "rnaseq", genefinder_rnaseq, select_rnaseq, SRscore_rnaseq, colnames_rnaseq, rnaseqBreaks, rnaseqColor)
+})

ui.R

@@ -0,0 +1,142 @@
+ui <- dashboardPage(
+  
+  dashboardHeader(title = "AtSRGA"),
+  
+  dashboardSidebar(
+    sidebarMenu(
+      menuItem("Home", tabName = "Home", icon = icon("home")),
+      menuItem("Microarray", tabName = "Microarray",
+               menuSubItem("Atlas", tabName = "Atlasm"),
+               menuSubItem("Template Matching", tabName = "TemplateMatchingm")
+               ),
+      menuItem("RNA-Seq", tabName = "RNA-Seq",
+               menuSubItem("Atlas", tabName = "Atlasr"),
+               menuSubItem("Template Matching", tabName = "TemplateMatchingr")
+               ),
+      menuItem("Help", tabName = "Help")
+    )
+  ),
+  
+  dashboardBody(
+    tags$style(type = "text/css",
+               ".shiny-output-error { visibility: hidden; }",
+               ".shiny-output-error:before { visibility: hidden; }"
+    ),
+    tabItems(
+      ## ======================================================== ##
+      ## Menu : Home
+      ## ======================================================== ##
+      tabItem(tabName = "Home",
+              titlePanel("Wellcome to AtSRGA")
+      ),    
+      ## ======================================================== ##
+      ## Menu : Microarray
+      ## ======================================================== ##
+      ## ======================================== ##
+      ## Sub Menu : Atlas
+      ## ======================================== ##
+      tabItem(tabName = "Atlasm",
+              tabBox(
+                title = "",
+                width = "100%",
+                tabPanel("Overview", overviewUI("microarray")),
+                tabPanel("ABA", stressUI("ABAm")),
+                tabPanel("cold", stressUI("coldm")),
+                tabPanel("DC3000", stressUI("DC3000m")),
+                tabPanel("drought", stressUI("droughtm")),
+                tabPanel("heat", stressUI("heatm")),
+                tabPanel("highlight", stressUI("highlightm")),
+                tabPanel("hypoxia", stressUI("hypoxiam")),
+                tabPanel("osmotic", stressUI("osmoticm")),
+                tabPanel("oxidation", stressUI("oxidationm")),
+                tabPanel("salt", stressUI("saltm")),
+                tabPanel("wound", stressUI("woundm"))
+              )
+      ),
+      ## ======================================== ##
+      ## Sub Menu : Template Matching
+      ## ======================================== ##
+      tabItem(tabName = "TemplateMatchingm",
+              box(
+                title = "",
+                width = "100%",
+                TemplateMatchUI("microarray")
+              )
+      ),
+      ## ========================================================= ##
+      ## Menu : RNA-Seq
+      ## ========================================================= ##
+      ## ======================================== ##
+      ## Sub Menu : Atlas
+      ## ======================================== ##
+      tabItem(tabName = "Atlasr",
+              tabBox(
+                title = "",
+                width = "100%",
+                tabPanel("Overview", overviewUI("rnaseq")),
+                tabPanel("ABA", stressUI("ABAr")),
+                tabPanel("cold", stressUI("coldr")),
+                tabPanel("DC3000", stressUI("DC3000r")),
+                tabPanel("heat", stressUI("heatr")),
+                tabPanel("drought", stressUI("droughtr")),
+                tabPanel("highlight", stressUI("highlightr")),
+                tabPanel("hypoxia", stressUI("hypoxiar")),
+                tabPanel("osmotic", stressUI("osmoticr")),
+                tabPanel("oxidation", stressUI("oxidationr")),
+                tabPanel("salt", stressUI("saltr")),
+                tabPanel("wound", stressUI("woundr"))
+              )
+      ),
+      ## ======================================== ##
+      ## Sub Menu : Template Matching
+      ## ======================================== ##
+      tabItem(tabName = "TemplateMatchingr",
+              box(
+                title = "",
+                width = "100%",
+                TemplateMatchUI("rnaseq")
+              )
+      ),
+      ## ======================================================== ##
+      ## Menu : Help
+      ## ======================================================== ##
+      tabItem(tabName = "Help",
+              box(
+                title = "",
+                width = "100%",
+                h1("Tutorial"),
+                br(),
+                HTML("<h4>Please see ",
+                     "<a href = https://github.com/fusk-kpu/StressResponseGenesAtlas/raw/main/AtSRGA_tutorial_en.pdf > our tutorial file. </a>"),
+                br(),
+                br(),
+                br(),
+                br(),
+                h1("Contact us"),
+                br(),
+                HTML("<h4>To get in contact with our group, please visit : ",
+                     "<a href = https://www.kpu-g.com/english > https://www.kpu-g.com/english </a>"),
+                br(),
+                br(),
+                br(),
+                br(),
+                h1("Report bugs"),
+                br(),
+                HTML("<h4>The R code for this application is available on ",
+                     "<a href = https://github.com/fusk-kpu/StressResponseGenesAtlas >  Github </a>",
+                     ". <br> To report bugs and/or request features, please use the following GitHub issue channel : <br><br>
+                <a href = https://github.com/fusk-kpu/StressResponseGenesAtlas/issues > https://github.com/fusk-kpu/StressResponseGenesAtlas/issues </a>"),
+                br(),
+                br(),
+                br(),
+                br(),
+                h1("Citation"),
+                br(),
+                HTML("<h4>If you find <strong>AtSRGA</strong>, useful, please consider citing our publication : <br><br>
+                Coming soon :)"),
+                img(src = "hexsticker_AtSRGA.png", width = "250px", height = "300px",
+                    style="position:absolute; top:50px; right:50px;")
+              ))
+      )
+  )
+)