95_waterfall_plot_bugs

R/waterfall_plot.R

@@ -21,6 +21,7 @@
 #' @importFrom ggplot2 aes facet_wrap geom_col geom_hline ggplot labs scale_fill_manual scale_x_discrete scale_y_continuous theme_minimal
 #' @importFrom rlang check_dots_empty
 #' @importFrom scales breaks_width label_percent
+#' @importFrom cli cli_warn
 #'
 #' @examples
 #' db = grstat_example(N=50)
@@ -76,6 +77,14 @@ waterfall_plot = function(data, ...,
 
   db_wf = data %>%
     rename(shape=any_of2(shape), resp=all_of(fill), y=all_of(y)) %>%
+    {
+      na_rows = which(is.na(.$y))
+      na_y = length(na_rows)
+      if(na_y > 0){
+        if(warnings) cli_warn("{.fun waterfall_plot} will ignore {na_y} observation{?s} with missing {.var {y}} and subjid : {.val { . $subjid[na_rows]}}.")
+        filter(., !is.na(y))
+      } else .
+    } %>%
     mutate(subjid = forcats::fct_reorder2(as.character(subjid),
                                           as.numeric(resp), y))
 

tests/testthat/test-best_response.R

@@ -11,39 +11,4 @@ test_that("calc_best_response", {
 })
 
 
-test_that("waterfall_plot", {
-  local_options(grstat_lifecycle_verbosity="quiet")
-
-  db = grstat_example(N=50)
-  data_best_resp = calc_best_response(db$recist)
-
-  #simple example
-  p1 = waterfall_plot(data_best_resp)
-  vdiffr::expect_doppelganger("waterfall-plot-default", p1)
-
-  #facet by arm
-  p2 = data_best_resp %>%
-    left_join(db$enrolres, by="subjid") %>%
-    waterfall_plot(arm="ARM")
-  vdiffr::expect_doppelganger("waterfall-plot-arms", p2)
 
-
-  #add symbols
-  #use the NA level to not show the case
-  set.seed(0)
-  data_symbols = db$recist %>%
-    summarise(new_lesion=ifelse(any(rcnew=="Yes", na.rm=TRUE), "New lesion", NA),
-              random=cut(runif(1), breaks=c(0,0.05,0.1,1), labels=c("A", "B", NA)),
-              .by=subjid)
-
-  p3 = data_best_resp %>%
-    left_join(data_symbols, by="subjid") %>%
-    waterfall_plot(shape="new_lesion")
-  vdiffr::expect_doppelganger("waterfall-plot-shape1", p3)
-
-  p4 = data_best_resp %>%
-    left_join(data_symbols, by="subjid") %>%
-    waterfall_plot(shape="random") +
-    labs(shape="Event")
-  vdiffr::expect_doppelganger("waterfall-plot-shape2", p4)
-})

tests/testthat/test-waterfall-plot.R

@@ -0,0 +1,51 @@
+test_that("waterfall_plot", {
+  local_options(grstat_lifecycle_verbosity="quiet")
+
+  db = grstat_example(N=50)
+  data_best_resp = calc_best_response(db$recist)
+
+  #simple example
+  p1 = waterfall_plot(data_best_resp)
+  vdiffr::expect_doppelganger("waterfall-plot-default", p1)
+
+  #facet by arm
+  p2 = data_best_resp %>%
+    left_join(db$enrolres, by="subjid") %>%
+    waterfall_plot(arm="ARM")
+  vdiffr::expect_doppelganger("waterfall-plot-arms", p2)
+
+
+  #add symbols
+  #use the NA level to not show the case
+  set.seed(0)
+  data_symbols = db$recist %>%
+    summarise(new_lesion=ifelse(any(rcnew=="Yes", na.rm=TRUE), "New lesion", NA),
+              random=cut(runif(1), breaks=c(0,0.05,0.1,1), labels=c("A", "B", NA)),
+              .by=subjid)
+
+  p3 = data_best_resp %>%
+    left_join(data_symbols, by="subjid") %>%
+    waterfall_plot(shape="new_lesion")
+  vdiffr::expect_doppelganger("waterfall-plot-shape1", p3)
+
+  p4 = data_best_resp %>%
+    left_join(data_symbols, by="subjid") %>%
+    waterfall_plot(shape="random") +
+    labs(shape="Event")
+  vdiffr::expect_doppelganger("waterfall-plot-shape2", p4)
+
+  set.seed(123)
+  data_na =
+    data_best_resp %>%
+    dplyr::mutate(
+      target_sum_diff_first = runif(n(), -0.6, 0.3),
+      target_sum_diff_first = replace(target_sum_diff_first, c(1, 3, 10), NA)
+    )
+
+  expect_warning(
+    p <- waterfall_plot(data_na, warnings = TRUE),
+    regexp = "ignore"
+  )
+
+
+})