From 7d4142db1f0c59e7756c9147a6b722ca3fd05b47 Mon Sep 17 00:00:00 2001
From: Andrei Martins <92amartins@gmail.com>
Date: Thu, 25 Apr 2024 13:27:17 -0300
Subject: [PATCH] fix: ggparcoord anyClass ordering with missing values in data

---
 NEWS.md                          |  2 ++
 R/ggparcoord.R                   |  1 +
 tests/testthat/test-ggparcoord.R | 11 +++++++++++
 3 files changed, 14 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 12445271a..dc59905f6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
 # GGally (development version)
 
+* Fix anyClass ordering in ggparcoord when data has missing values (#500)
+
 # GGally 2.2.1
 
 * Fix compatibility with ggplot2 3.5.0 (@teunbrand, #481)
diff --git a/R/ggparcoord.R b/R/ggparcoord.R
index ad6cf2ad2..fde5d737a 100644
--- a/R/ggparcoord.R
+++ b/R/ggparcoord.R
@@ -396,6 +396,7 @@ ggparcoord <- function(
     }
 
     data <- data[dataCompleteCases, ]
+    saveData2 <- saveData2[dataCompleteCases, ]
   } else if (tolower(missing) %in% c("mean", "median", "min10", "random")) {
     missingFns <- list(
       mean = function(x) {
diff --git a/tests/testthat/test-ggparcoord.R b/tests/testthat/test-ggparcoord.R
index 2cf67f8b1..c6d6e1e3a 100644
--- a/tests/testthat/test-ggparcoord.R
+++ b/tests/testthat/test-ggparcoord.R
@@ -227,6 +227,17 @@ test_that("order", {
   }
 })
 
+test_that("missing and order(anyClass)", {
+  ds2 <- diamonds.samp
+  ds2[3, 1] <- NA
+  missing_options <- c("exclude", "mean", "median", "min10", "random")
+
+  for (missing in missing_options) {
+    p <- ggparcoord(data = ds2, columns = c(1, 5:10), groupColumn = 2, missing = missing, order = "anyClass")
+  }
+  expect_true(TRUE)
+})
+
 test_that("basic", {
   # no color supplied
   p <- ggparcoord(data = diamonds.samp, columns = c(1, 5:10))