separate observes #106

R/kinetics.R

@@ -500,7 +500,7 @@ plot_kinetics <- function(kin_dat,
 
   }
 
-  kin_plot
+  return(HaDeXify(kin_plot))
 }
 
 #' Plot differential uptake curve
@@ -684,6 +684,6 @@ plot_differential_uptake_curve <- function(diff_uptake_dat = NULL,
 
   }
 
-  diff_kin_plot
+  return(HaDeXify(diff_kin_plot))
 
 }

R/p_plots.R

@@ -148,7 +148,7 @@ plot_volcano <- function(p_dat,
 
   }
 
-  return(volcano_plot)
+  return(HaDeXify(volcano_plot))
 
 }
 
@@ -242,6 +242,6 @@ plot_manhattan <- function(p_dat,
       geom_hline(yintercept = confidence_limit, linetype = "dashed") 
   }
 
-  manhattan_plot
+  return(HaDeXify(manhattan_plot))
 
 }

R/plot_coverage.R

@@ -37,7 +37,7 @@ plot_coverage <- function(dat,
                           protein = dat[["Protein"]][1],
                           states = dat[["State"]][1]){
 
-  dat %>%
+  cov_plot <- dat %>%
     filter(Protein == protein) %>%
     select(Start, End, State) %>%
     filter(State %in% states) %>%
@@ -54,4 +54,6 @@ plot_coverage <- function(dat,
     theme(axis.ticks.y = element_blank(),
           axis.text.y = element_blank())
 
+  return(HaDeXify(cov_plot))
+
 }

R/plot_position_frequency.R

@@ -46,8 +46,10 @@ plot_position_frequency <- function(dat,
     group_by(x) %>% 
     summarise(coverage = length(x)) 
 
-  ggplot(coverage_df, aes(x = x, y = coverage)) +
+  pos_freq_plot <- ggplot(coverage_df, aes(x = x, y = coverage)) +
     geom_col(width = 1) +
     labs(x = 'Position', y = 'Position frequency in peptides') +
     theme(legend.position = "none")
+
+  return(HaDeXify(pos_freq_plot))
 }

R/uptake_plots.R

@@ -80,7 +80,7 @@ plot_state_comparison <- function(dat,
                          value = dat[[value]],
                          err_value = dat[[err_value]])
 
-  ggplot(data = plot_dat) +
+  state_comp_plot <- ggplot(data = plot_dat) +
     geom_segment(data = plot_dat, aes(x = Start, y = value, xend = End, yend = value, color = State)) +
     geom_errorbar(data = plot_dat, aes(x = Med_Sequence, ymin = value - err_value, ymax = value + err_value, color = State)) +
     labs(title = title,
@@ -89,6 +89,8 @@ plot_state_comparison <- function(dat,
     theme(legend.position = "bottom",
           legend.title = element_blank())
 
+  return(HaDeXify(state_comp_plot))
+
 }
 
 #' Butterfly plot
@@ -201,7 +203,7 @@ plot_butterfly <- function(butterfly_dat,
 
   }
 
-  return(butterfly_plot)
+  return(HaDeXify(butterfly_plot))
 
 }
 
@@ -312,6 +314,6 @@ plot_chiclet <- function(chiclet_dat,
 
   } 
 
-  return(chiclet_plot)
+  return(HaDeXify(chiclet_plot))
 
 }

inst/HaDeX/server/tab_butterfly.R

@@ -8,6 +8,12 @@ observe({
                     inputId = "butt_state",
                     choices = states_chosen_protein(),
                     selected = states_chosen_protein()[1])
+
+})
+
+##
+
+observe({
 
   if(input[["butt_fractional"]]){
 
@@ -34,6 +40,11 @@ observe({
                     inputId = "butt_time_0",
                     choices = times_from_file()[times_from_file() < 99999],
                     selected = min(times_from_file()[times_from_file() > 0]))
+})
+
+##
+
+observe({
 
   updateSelectInput(session,
                     inputId = "butt_time_100",
@@ -43,6 +54,20 @@ observe({
 
 ##
 
+observe({
+
+  max_x <- max(butterfly_dataset()[["ID"]])
+  min_x <- min(butterfly_dataset()[["ID"]])
+
+  updateSliderInput(session,
+                    inputId = "butt_x_range",
+                    min = min_x,
+                    max = max_x,
+                    value = c(min_x, max_x))
+})
+
+##
+
 observe({
 
   if(input[["butt_fractional"]]){
@@ -56,15 +81,6 @@ observe({
     min_y <- floor(min(butterfly_dataset()[["deut_uptake"]], butterfly_dataset()[["theo_deut_uptake"]], na.rm = TRUE)) - 1
   }
 
-  max_x <- max(butterfly_dataset()[["ID"]])
-  min_x <- min(butterfly_dataset()[["ID"]])
-
-  updateSliderInput(session,
-                    inputId = "butt_x_range",
-                    min = min_x,
-                    max = max_x,
-                    value = c(min_x, max_x))
-
   updateSliderInput(session,
                     inputId = "butt_y_range",
                     min = min_y - 5,

inst/HaDeX/server/tab_butterfly_differential.R

@@ -8,12 +8,22 @@ observe({
                     inputId = "butt_diff_state_1",
                     choices = states_chosen_protein(),
                     selected = states_chosen_protein()[1])
+})
+
+##
 
+observe({
+
   updateSelectInput(session,
                     inputId = "butt_diff_state_2",
                     choices = states_chosen_protein(),
                     selected = states_chosen_protein()[length(states_chosen_protein())])
+})
 
+##
+
+observe({
+
   if(input[["butt_diff_fractional"]]){
 
     times_t <- times_from_file()[times_from_file() > as.numeric(input[["butt_diff_time_0"]]) & times_from_file() < as.numeric(input[["butt_diff_time_100"]])]
@@ -38,7 +48,12 @@ observe({
                     inputId = "butt_diff_time_0",
                     choices = times_from_file()[times_from_file() < 99999],
                     selected = min(times_from_file()[times_from_file() > 0]))
+})
 
+##
+
+observe({
+
   updateSelectInput(session,
                     inputId = "butt_diff_time_100",
                     choices = times_with_control(),
@@ -55,7 +70,12 @@ observe({
                     input[["butt_diff_theory"]] ~ paste0("Thereotical butterfly differential plot between ", input[["butt_diff_state_1"]], " and ", input[["butt_diff_state_2"]]),
                     !input[["butt_diff_theory"]] ~ paste0("Butterfly differential plot between ", input[["butt_diff_state_1"]], " and ", input[["butt_diff_state_2"]])
                   ))
+})
+
+##
 
+observe({
+
   updateTextInput(session,
                   inputId = "butterflyDifferential_plot_y_label",
                   value = case_when(
@@ -70,17 +90,6 @@ observe({
 
 observe({
 
-  if (input[["butt_diff_fractional"]]) {
-
-    max_y <- ceiling(max(butt_diff_dataset()[["diff_frac_deut_uptake"]], butt_diff_dataset()[["diff_theo_frac_deut_uptake"]], na.rm = TRUE)) + 1
-    min_y <- floor(min(butt_diff_dataset()[["diff_frac_deut_uptake"]], butt_diff_dataset()[["diff_theo_frac_deut_uptake"]], na.rm = TRUE)) - 1
-
-  } else {
-
-    max_y <- ceiling(max(butt_diff_dataset()[["diff_deut_uptake"]], butt_diff_dataset()[["diff_theo_deut_uptake"]], na.rm = TRUE)) + 1
-    min_y <- floor(min(butt_diff_dataset()[["diff_deut_uptake"]], butt_diff_dataset()[["diff_theo_deut_uptake"]], na.rm = TRUE)) - 1
-  }
-
   max_x <- max(butt_diff_dataset()[["ID"]])
   min_x <- min(butt_diff_dataset()[["ID"]])
 
@@ -92,6 +101,23 @@ observe({
     value = c(min_x, max_x)
   )
 
+})
+
+##
+
+observe({
+
+  if (input[["butt_diff_fractional"]]) {
+
+    max_y <- ceiling(max(butt_diff_dataset()[["diff_frac_deut_uptake"]], butt_diff_dataset()[["diff_theo_frac_deut_uptake"]], na.rm = TRUE)) + 1
+    min_y <- floor(min(butt_diff_dataset()[["diff_frac_deut_uptake"]], butt_diff_dataset()[["diff_theo_frac_deut_uptake"]], na.rm = TRUE)) - 1
+
+  } else {
+
+    max_y <- ceiling(max(butt_diff_dataset()[["diff_deut_uptake"]], butt_diff_dataset()[["diff_theo_deut_uptake"]], na.rm = TRUE)) + 1
+    min_y <- floor(min(butt_diff_dataset()[["diff_deut_uptake"]], butt_diff_dataset()[["diff_theo_deut_uptake"]], na.rm = TRUE)) - 1
+  }
+
   updateSliderInput(
     session,
     inputId = "butt_diff_y_range",

inst/HaDeX/server/tab_chiclet.R

@@ -34,6 +34,11 @@ observe({
                     inputId = "chic_time_0",
                     choices = times_from_file()[times_from_file() < 99999],
                     selected = min(times_from_file()[times_from_file() > 0]))
+})
+
+##
+
+observe({
 
   updateSelectInput(session,
                     inputId = "chic_time_100",

inst/HaDeX/server/tab_chiclet_differential.R

@@ -8,11 +8,21 @@ observe({
                     inputId = "chic_diff_state_1",
                     choices = states_chosen_protein(),
                     selected = states_chosen_protein()[1])
+})
+
+##
+
+observe({
 
   updateSelectInput(session,
                     inputId = "chic_diff_state_2",
                     choices = states_chosen_protein(),
                     selected = states_chosen_protein()[length(states_chosen_protein())])
+})
+
+##
+
+observe({
 
   if(input[["chic_diff_fractional"]]){
 
@@ -38,6 +48,11 @@ observe({
                     inputId = "chic_diff_time_0",
                     choices = times_from_file()[times_from_file() < 99999],
                     selected = min(times_from_file()[times_from_file() > 0]))
+})
+
+##
+
+observe({
 
   updateSelectInput(session,
                     inputId = "chic_diff_time_100",

inst/HaDeX/server/tab_comparison.R

@@ -73,7 +73,12 @@ observe({
                     input[["theory"]] ~ paste0("Theoretical deuterium uptake in ", input[["time_t"]], " min for ", input[["chosen_protein"]]),
                     !input[["theory"]]  ~ paste0("Deuterium uptake in ", input[["time_t"]], " min for ", input[["chosen_protein"]])
                   ))
+})
+
+##
 
+observe({
+
   updateTextInput(session,
                   inputId = "comparison_plot_y_label",
                   value = case_when(
@@ -149,7 +154,12 @@ observe({
                     inputId = "plot_range",
                     max = max_range(),
                     value = c(1, max_range()))
+})
 
+##
+
+observe({
+
   updateSliderInput(session,
                     inputId = "plot_x_range",
                     max = max_range(),
@@ -208,25 +218,6 @@ comparison_plot_colors <- reactive({
 
 output[["states_colors"]] <- renderUI({
 
-  # colorInput <- function(inputId, label, value = "", width = NULL, placeholder = NULL) {
-  #   '%BAND%' <- function (x, y) {
-  #     if (!is.null(x) && !is.na(x))
-  #       if (!is.null(y) && !is.na(y))
-  #         return(y)
-  #     return(NULL)
-  #   }
-  #   value <- restoreInput(id = inputId, default = value)
-  #   if(!is.null(value))
-  #     div(class = "form-group shiny-input-container",
-  #         style = paste(if (value != "") paste0("background-color=: ", validateCssUnit(width), ";"),
-  #                       if (!is.null(width)) paste0("width: ", validateCssUnit(width), ";")
-  #         ),
-  #         label %BAND%
-  #         tags$label(label, `for` = inputId), tags$input(id = inputId,
-  #                                                        type = "text", class = "form-control", value = value,
-  #                                                        placeholder = placeholder))
-  # }
-
   lapply(1:length(states_from_file()), function(i) {
     textInput(inputId = paste0(states_from_file()[i], "_color"),
               label = paste(states_from_file()[i], " color"),

inst/HaDeX/server/tab_differential.R

@@ -39,6 +39,12 @@ observe({
                     input[["theory"]] ~ paste0("Theoretical deuterium uptake difference in ", input[["time_t"]], " min between ", gsub("_", " ", input[["diff_state_1"]]), " and ", gsub("_", " ", input[["diff_state_2"]]), " for ", input[["chosen_protein"]]),
                     !input[["theory"]] ~ paste0("Deuterium uptake difference in ", input[["time_t"]], " min between ", gsub("_", " ", input[["diff_state_1"]]), " and ", gsub("_", " ", input[["diff_state_2"]]), " for ", input[["chosen_protein"]])
                   ))
+
+})
+
+##
+
+observe({
 
   updateTextInput(session,
                   inputId = "woods_plot_y_label",
@@ -52,18 +58,25 @@ observe({
 
 observe({
 
-
   updateSelectInput(session,
                     inputId = "diff_state_1",
                     choices = states_chosen_protein(),
                     selected = states_chosen_protein()[1])
+})
+
+##
+
+observe({
 
   updateSelectInput(session,
                     inputId = "diff_state_2",
                     choices = states_chosen_protein(),
                     selected = states_chosen_protein()[length(states_chosen_protein())])
-
-
+})
+
+##
+
+observe({  
 
   updateSelectInput(session,
                     inputId = "confidence_level_2",