add censoring limits to shiny plots

seroanalytics · Nov 20, 2024 · bd40935 · bd40935
1 parent 75bbd0b
commit bd40935
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Showing 2 changed files with 12 additions and 8 deletions.
diff --git a/R/inspect-model.R b/R/inspect-model.R
@@ -96,7 +96,9 @@ inspect_model <- function(mod, private) {
       prior_code(input)
     })
     output$prior_predicted <- plotly::renderPlotly({
-      plotly::ggplotly(plot(prior()))
+      plotly::style(plotly::ggplotly(plot(prior(),
+                            upper_censoring_limit = private$stan_input_data$upper_censoring_limit,
+                            lower_censoring_limit = private$stan_input_data$lower_censoring_limit)), textposition = "right")
     })
 
     # model inputs
@@ -135,13 +137,17 @@ inspect_model <- function(mod, private) {
       if (is.null(selected) || selected == "None") {
         selected <- character(0)
       }
-      plot_sero_data(data(), ncol = cols(), covariates = selected) +
+      plot_sero_data(data(),
+                     ncol = cols(),
+                     covariates = selected,
+                     upper_censoring_limit = private$stan_input_data$upper_censoring_limit,
+                     lower_censoring_limit = private$stan_input_data$lower_censoring_limit) +
         theme(plot.margin = unit(c(1, 0, 0, 0), "cm"))
     })
 
     output$data <- plotly::renderPlotly({
       if (nrow(data()) > 0) {
-        gp <- plotly::ggplotly(plot_inputs())
+        gp <- plotly::style(plotly::ggplotly(plot_inputs()), textposition="right")
         if (selected_covariate() != "None") {
           return(facet_strip_bigger(gp, 30))
         } else {

diff --git a/R/plot.R b/R/plot.R
@@ -56,10 +56,8 @@ plot.biokinetics_priors <- function(x,
       geom_point(data = dat, size = 0.5,
                  aes(x = time_since_last_exp,
                      y = value))
-
-    plot <- add_limits(plot, upper_censoring_limit, lower_censoring_limit)
   }
-  plot
+  add_limits(plot, upper_censoring_limit, lower_censoring_limit)
 }
 
 #' @title Plot serological data
@@ -157,7 +155,7 @@ add_limits <- function(plot, upper_censoring_limit, lower_censoring_limit) {
                  linetype = 'dotted') +
       annotate("text", x = 1,
                y = lower_censoring_limit,
-               label = "Lower detection limit",
+               label = "Lower censoring limit",
                vjust = -0.5,
                hjust = 0,
                size = 3)
@@ -168,7 +166,7 @@ add_limits <- function(plot, upper_censoring_limit, lower_censoring_limit) {
                  linetype = 'dotted') +
       annotate("text", x = 1,
                y = upper_censoring_limit,
-               label = "Upper detection limit",
+               label = "Upper censoring limit",
                vjust = -0.5,
                hjust = 0,
                size = 3)