feat: add example using the poc data

R/tm_p_swimlane.R

@@ -1,17 +1,12 @@
-tm_p_swimlane <- function(label = "Swimlane Plot Module",
-                          geom_specs,
-                          title,
-                          color_manual = NULL,
-                          shape_manual = NULL,
-                          size_manual = NULL) {
+tm_p_swimlane <- function(label = "Swimlane Plot Module", geom_specs, title) {
   module(
     label = label,
     ui = ui_p_swimlane,
     server = srv_p_swimlane,
     datanames = "all",
     server_args = list(
-      geom_specs = geom_specs, title = title,
-      color_manual = color_manual, shape_manual = shape_manual, size_manual = size_manual
+      geom_specs = geom_specs,
+      title = title
     )
   )
 }
@@ -28,9 +23,6 @@ srv_p_swimlane <- function(id,
                            data,
                            geom_specs,
                            title = "Swimlane plot",
-                           color_manual,
-                           shape_manual,
-                           size_manual,
                            filter_panel_api) {
   moduleServer(id, function(input, output, session) {
     ggplot_call <- reactive({
@@ -72,8 +64,6 @@ srv_p_swimlane <- function(id,
   })
 }
 
-
-
 merge_selectors2 <- function() {
   lappl
 }

inst/poc_crf.R

@@ -0,0 +1,112 @@
+pkgload::load_all("teal")
+pkgload::load_all("teal.widgets")
+pkgload::load_all("teal.modules.general")
+
+# Example data
+data <- within(teal_data(), {
+  library(dplyr)
+  library(arrow)
+  library(forcats)
+  data_path <- "PATH_TO_DATA"
+
+  swimlane_ds <- read_parquet(file.path(data_path, "swimlane_ds.parquet")) |>
+    filter(!is.na(event_result), !is.na(event_study_day)) |>
+    mutate(subject = forcats::fct_reorder(as.factor(subject), event_study_day, .fun = max))
+  disposition <- swimlane_ds |>
+    filter(!is.na(event_study_day)) |>
+    filter(event_type == "disposition") |>
+    transmute(subject, event_type, catagory = event_result, study_day = event_study_day)
+
+  response_assessment <- swimlane_ds |>
+    filter(!is.na(event_study_day)) |>
+    filter(event_type == "response_assessment") |>
+    transmute(subject, event_type, catagory = event_result, study_day = event_study_day)
+
+  study_drug_administration <- swimlane_ds |>
+    filter(!is.na(event_study_day)) |>
+    filter(event_type == "study_drug_administration") |>
+    transmute(subject, event_type, catagory = event_result, study_day = event_study_day)
+
+  max_subject_day <- swimlane_ds |>
+    group_by(subject) |>
+    summarise(max_study_day = max(event_study_day))
+})
+
+color_manual <- c(
+  "DEATH" = "black",
+  "WITHDRAWAL BY SUBJECT" = "grey",
+  "PD (Progressive Disease)" = "red",
+  "SD (Stable Disease)" = "darkorchid4",
+  "MR (Minimal/Minor Response)" = "sienna4",
+  "PR (Partial Response)" = "maroon",
+  "VGPR (Very Good Partial Response)" = "chartreuse4",
+  "CR (Complete Response)" = "#3a41fc",
+  "SCR (Stringent Complete Response)" = "midnightblue"
+)
+shape_manual <- c(
+  "DEATH" = 4,
+  "WITHDRAWAL BY SUBJECT" = 5,
+  "PD (Progressive Disease)" = 8,
+  "SD (Stable Disease)" = 5,
+  "MR (Minimal/Minor Response)" = 5,
+  "PR (Partial Response)" = 5,
+  "VGPR (Very Good Partial Response)" = 5,
+  "CR (Complete Response)" = 5,
+  "SCR (Stringent Complete Response)" = 5
+)
+
+app <- init(
+  data = data,
+  modules = modules(
+    tm_data_table(),
+    tm_p_swimlane(
+      label = "Swimlane",
+      geom_specs = list(
+        list(
+          geom = str2lang("ggplot2::geom_bar"),
+          data = quote(max_subject_day),
+          mapping = list(y = quote(subject), x = quote(max_study_day)),
+          stat = "identity",
+          width = 0.1
+        ),
+        list(
+          geom = quote(geom_point),
+          data = quote(study_drug_administration),
+          mapping = list(
+            y = quote(subject), x = quote(study_day), color = quote(catagory), shape = quote(catagory)
+          )
+        ),
+        list(
+          geom = quote(geom_point),
+          data = quote(disposition),
+          mapping = list(
+            y = quote(subject), x = quote(study_day), color = quote(catagory), shape = quote(catagory)
+          )
+        ),
+        list(
+          geom = quote(geom_point),
+          data = quote(response_assessment),
+          mapping = list(
+            y = quote(subject), x = quote(study_day), color = quote(catagory), shape = quote(catagory)
+          )
+        ),
+        list(
+          geom = quote(scale_color_manual),
+          values = color_manual,
+          breaks = names(color_manual)
+        ),
+        list(
+          geom = quote(scale_shape_manual),
+          values = shape_manual,
+          breaks = names(shape_manual)
+        ),
+        list(
+          geom = quote(theme_minimal)
+        )
+      ),
+      title = "Swimlane Efficacy Plot"
+    )
+  )
+)
+
+shinyApp(app$ui, app$server)