From 2e17fe7e035eeecad994615769923680417c58b8 Mon Sep 17 00:00:00 2001
From: Sebastian Gibb <mail@sebastiangibb.de>
Date: Mon, 13 Jul 2015 19:27:01 +0200
Subject: [PATCH] .plotMsiSlice incorrectly used just the first z dimension if
 "combine=TRUE"

---
 DESCRIPTION                                  | 4 ++--
 NEWS                                         | 4 ++++
 R/plotMsiSlice-functions.R                   | 2 +-
 tests/testthat/test_plotMsiSlice-functions.R | 8 +++++---
 4 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4fbc501..0944bf8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MALDIquant
-Version: 1.12.5
-Date: 2015-07-12
+Version: 1.12.6
+Date: 2015-07-13
 Title: Quantitative Analysis of Mass Spectrometry Data
 Authors@R: c(person("Sebastian", "Gibb", role=c("aut", "cre"),
         email="mail@sebastiangibb.de"), person("Korbinian", "Strimmer",
diff --git a/NEWS b/NEWS
index fbb3137..7db8cf7 100644
--- a/NEWS
+++ b/NEWS
@@ -1,6 +1,10 @@
 RELEASE HISTORY OF THE "MALDIquant" PACKAGE
 ===========================================
 
+Version 1.12.6 [2015-07-13 Mon]:
+- BUGFIX: `.plotMsiSlice` just used the first center if "combine=TRUE";
+  affected functions: `plotMsiSlice`.
+
 Version 1.12.5 [2015-07-12 Sun]:
 - `calibratyIntensity`: gains a "range" argument for "median" and "PQN" as well;
   in 1.12 just "TIC" was supported.
diff --git a/R/plotMsiSlice-functions.R b/R/plotMsiSlice-functions.R
index 3e6c715..d47031d 100644
--- a/R/plotMsiSlice-functions.R
+++ b/R/plotMsiSlice-functions.R
@@ -39,7 +39,7 @@
     col <- x
 
     for (i in seq_len(d[3L])) {
-      col[,, i] <- .colorMatrix(.array2matrix(x), colRamp=colRampList[[i]],
+      col[,, i] <- .colorMatrix(.array2matrix(x, z=i), colRamp=colRampList[[i]],
                                 scale=scale)
     }
 
diff --git a/tests/testthat/test_plotMsiSlice-functions.R b/tests/testthat/test_plotMsiSlice-functions.R
index 6bac28d..abe3eaf 100644
--- a/tests/testthat/test_plotMsiSlice-functions.R
+++ b/tests/testthat/test_plotMsiSlice-functions.R
@@ -3,11 +3,13 @@ context(".plotMsiSlice")
 test_that(".array2matrix", {
   x1 <- array(1:12, dim=c(x=2, y=3, z=2))
   x2 <- array(1:12, dim=c(1, 12, 1))
-  r1 <- matrix(1:12, nrow=2, ncol=3)
-  r2 <- matrix(1:12, nrow=1, ncol=12)
+  r1 <- matrix(1:6, nrow=2, ncol=3)
+  r2 <- matrix(7:12, nrow=2, ncol=3)
+  r3 <- matrix(1:12, nrow=1, ncol=12)
 
   expect_identical(MALDIquant:::.array2matrix(x1), r1)
-  expect_identical(MALDIquant:::.array2matrix(x2), r2)
+  expect_identical(MALDIquant:::.array2matrix(x1, z=2), r2)
+  expect_identical(MALDIquant:::.array2matrix(x2), r3)
 })
 
 test_that(".colorMatrix", {