added templates for i2dash functions

inst/templates/geneView_wilson.Rmd

@@ -0,0 +1,186 @@
+
+### {{ title }}
+
+<!-- Component created on {{ date }} -->
+
+```{r}
+{{ env_id }} = readRDS("envs/{{ env_id }}.rds")
+
+is_shiny <- identical(knitr::opts_knit$get("rmarkdown.runtime"), "shiny")
+```
+
+```{r, eval=!is_shiny}
+# Parameters for wilson::create_geneview()
+# params <- list()
+"%ni%" <- Negate("%in%")
+additional_arguments <- {{ env_id }}$additional_arguments
+
+if("plot.type" %ni% names({{ env_id }}$additional_arguments)){
+  additional_arguments$plot.type <- "line"
+}
+if("facet.target" %ni% names({{ env_id }}$additional_arguments)){
+  additional_arguments$facet.target <- "gene"
+}
+if("facet.cols" %ni% names({{ env_id }}$additional_arguments)){
+  additional_arguments$facet.cols <- 3
+}
+if("color" %ni% names({{ env_id }}$additional_arguments)){
+  color <- RColorBrewer::brewer.pal(8, "Accent")
+  additional_arguments$color <- color
+}
+
+# force static
+additional_arguments$plot.method <- "static"
+
+# set variables
+countTable <- {{ env_id }}$countTable
+group_by <- {{ env_id }}$group_by[1]
+
+# create data.tables "data" and "grouping" from provided data
+data <- data.table::data.table("features" = rownames(countTable), countTable)
+grouping <- data.table::data.table("keys" = colnames(countTable), "factor" = group_by[[1]])
+
+additional_arguments$data <- data
+additional_arguments$grouping <- grouping
+
+# Provide data for download
+#i2dash::embed_var(data)
+
+# Render plot
+output_list <- do.call(wilson::create_geneview, additional_arguments)
+plot <- output_list$plot
+plot
+```
+
+```{r, eval=is_shiny}
+#########
+library(shinyWidgets)
+#############
+
+ui_list <- list()
+
+# select type of plot
+ui_list <- rlist::list.append(ui_list,
+                                selectInput("select_type_{{ env_id }}", label = "Type of Plot:",
+                                            choices = c("line", "box", "violin", "bar"), selected = "line"))
+
+# subset features
+ui_list <- rlist::list.append(ui_list,
+                                selectInput("select_subset_{{ env_id }}",
+                                  label = "Select features:",
+                                  choices = rownames({{ env_id }}$countTable),
+                                  multiple = TRUE)
+                              )
+
+# selection field for group_by
+if ({{ env_id }}$group_by_selection){
+  ui_list <- rlist::list.append(ui_list,
+                                selectInput("select_group_by_{{ env_id }}", label = "Select grouping:",
+                                            choices = names({{ env_id }}$group_by)))
+}
+# selection grouping by
+ui_list <- rlist::list.append(ui_list,
+                                selectInput("select_by_{{ env_id }}",
+                                  label = "Grouping by:",
+                                  choices = c("gene", "condition"),
+                                  selected = "gene",
+                                  multiple = FALSE)
+                              )
+# selection column number of plot
+ui_list <- rlist::list.append(ui_list,
+                                sliderInput("colnumber_{{ env_id }}", label = h3("Plot columns:"), min = 1, max = 7, value = 3)
+                              )
+
+# Download link
+ui_list <- rlist::list.append(ui_list, tags$div(tags$br(), downloadButton('downloadData_{{ env_id }}', 'Download data')))
+
+#
+# Create reactive data table
+#
+df_{{ env_id }} <- shiny::reactive({
+  
+  # Parameters for wilson::create_geneview()
+  # params <- list()
+  "%ni%" <- Negate("%in%")
+  additional_arguments <- {{ env_id }}$additional_arguments
+  
+    # type of plot
+  additional_arguments$plot.type <- input$select_type_{{ env_id }}
+  
+  # type of grouping by
+  additional_arguments$facet.target <- input$select_by_{{ env_id }}
+  
+  # number of columns in plot
+  additional_arguments$facet.cols <- input$colnumber_{{ env_id }}
+  
+  if("color" %ni% names({{ env_id }}$additional_arguments)){
+    color <- RColorBrewer::brewer.pal(8, "Accent")
+    additional_arguments$color <- color
+  }
+  
+  # force static
+  additional_arguments$plot.method <- "static"
+  
+  # Set values for 'group_by'
+  if( !{{ env_id }}$group_by_selection ) {
+    group_by <- {{ env_id }}$group_by[1]
+  } else {
+    group_by <- {{ env_id }}$group_by[input$select_group_by_{{ env_id }}]
+  }
+  
+  # subset countTable by chosen features
+  countTable <- {{ env_id }}$countTable
+
+  if(!is.null(input$select_subset_{{ env_id }})){
+    subset_features <- input$select_subset_{{ env_id }}
+    if(length(subset_features) > 1){
+      countTable <- countTable[subset_features,]
+    } else if(length(subset_features) == 1){
+      countTable <- countTable[subset_features,,drop = FALSE]
+    }
+  }
+  
+  # create data.tables "data" and "grouping" from provided data
+  data <- data.table::data.table("features" = rownames(countTable), countTable)
+  grouping <- data.table::data.table("keys" = colnames(countTable), "factor" = group_by[[1]])
+
+  additional_arguments$data <- data
+  additional_arguments$grouping <- grouping
+  return(list("params" = additional_arguments, "data" = data, "grouping" = grouping))
+})
+
+#
+# Download
+#
+############
+# To do: provide both data.frames for download
+output$downloadData_{{ env_id }} <- downloadHandler(
+  filename =  paste('data-', Sys.Date(), '.csv', sep=''),
+  content = function(file) {
+    write.csv(df_{{ env_id }}()$data, file)
+  }
+)
+
+#
+# Output
+#
+output$plot_{{ env_id }} <- shiny::renderPlot({
+    if(!is.null(input$select_subset_{{ env_id }})){
+      output_list <- do.call(wilson::create_geneview, df_{{ env_id }}()$params)
+      plot <- output_list$plot
+      plot
+    }
+    # convert to plotly object for automatic resizing
+    
+})
+
+#
+# Layout of component
+#
+shiny::fillRow(flex = c(NA, 1),
+        dropdownButton(do.call(shiny::inputPanel, ui_list),
+                       circle = TRUE, status = "danger", icon = icon("gear"), width = "300px",
+                       tooltip = tooltipOptions(title = "Click, to change plot settings:")),
+        plotOutput("plot_{{ env_id }}")
+)
+```