From d06b32b33afa619a4edd2ad95644c59b6108d63e Mon Sep 17 00:00:00 2001
From: Dillon Hammill <dillon.hammill@ozette.com>
Date: Tue, 14 May 2024 08:54:51 +1000
Subject: [PATCH] Support instrument ranges in cyto_plot_calibarte().

---
 DESCRIPTION                |  2 +-
 NEWS.md                    |  6 +++++-
 R/cyto_plot-helpers.R      | 36 ++++++++++++++++++++++++++++--------
 man/cyto_plot_calibrate.Rd | 14 ++++++++------
 4 files changed, 42 insertions(+), 16 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d735cf51..1b0d8344 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CytoExploreR
 Type: Package
 Title: Interactive Analysis of Cytometry Data
-Version: 2.0.5
+Version: 2.0.6
 Date: 2024-04-10
 Authors@R: c(
   person("Dillon", "Hammill", role = c("aut", "cre"), email = "Dillon.Hammill@anu.edu.au"),
diff --git a/NEWS.md b/NEWS.md
index b74fd9bc..3e691752 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,11 @@
-# CytoExploreR 2.0.6 (pre-release)
+# CytoExploreR 2.0.7 (pre-release)
 
 * The behavior of `cyto_merge_by()` when `merge_by = NA` has changed from collapsing all samples to instead split samples individually. This is because splitting by `name` may not always work in cases where multiple samples share the same file names. This change requires updates to openCyto which should be re-installed when updating to the new version of CytoExploreR.
 
+# CytoExploreR 2.0.6
+
+* `cyto_plot_calibrate()` can now use the full instrument ranges for calibration through `type = "instrument"`.
+
 # CytoExploreR 2.0.5
 
 * `cyto_import()` has gained a logical `nodes` argument that allows for bypassing of the unique nodes test and renaming (it can be temperamental for complex node names).
diff --git a/R/cyto_plot-helpers.R b/R/cyto_plot-helpers.R
index 1b6b3e92..8978a1cc 100644
--- a/R/cyto_plot-helpers.R
+++ b/R/cyto_plot-helpers.R
@@ -2035,12 +2035,14 @@ cyto_plot_layout <- function(...){
 #'   extract samples that should be used to calibrate the channels, set to NULL
 #'   by default to calibrate channels using data from all samples.
 #' @param type indicates the type of calibration to perform, options include
-#'   \code{"range"} or \code{"quantile"}, set to \code{"quantile"} by default.
-#'   Range calibration simply uses the full range of values across samples for
-#'   the calibration. Quantile calibration computes an lower and upper quantile
-#'   for each channel, values falling outside the calibration range are assigned
-#'   the bottom or top colour. Alternatively, users can also supply their own
-#'   custom calibration function to \code{type} that accepts a matrix.
+#'   \code{"instrument"}, \code{"range"} or \code{"quantile"}, set to
+#'   \code{"quantile"} by default. Instrument calibartion uses the full
+#'   instrument range in each channel for calibration. Range calibration simply
+#'   uses the full range of values across samples for the calibration. Quantile
+#'   calibration computes an lower and upper quantile for each channel, values
+#'   falling outside the calibration range are assigned the bottom or top
+#'   colour. Alternatively, users can also supply their own custom calibration
+#'   function to \code{type} that accepts a matrix.
 #' @param probs vector of lower and upper probabilities passed to
 #'   \code{stats:quantile} to compute quantiles, set to \code{c(0.01, 0.99)} by
 #'   default.
@@ -2183,8 +2185,26 @@ cyto_plot_calibrate <- function(x,
       }
       # ONLY COMPUTE LIMITS IF NOT SUPPLIED
       if(any(is.na(z))) {
-        # RANGE
-        if(grepl("^r", type, ignore.case = TRUE)) {
+        # INSTRUMENT|MACHINE
+        if(grepl("^i|^m", type, ignore.case = TRUE)) {
+          res <- cyto_apply(
+            x,
+            function(w) {
+              range(
+                w,
+                "instrument"
+              )
+            },
+            select = 1,
+            parent = parent,
+            channels = channels[cnt],
+            input = "cytoframe",
+            inverse = FALSE,
+            copy = FALSE,
+            ...
+          )
+        # RANGE|DATA
+        } else if(grepl("^r|^d", type, ignore.case = TRUE)) {
           res <- cyto_apply(
             x,
             "cyto_stat_range",
diff --git a/man/cyto_plot_calibrate.Rd b/man/cyto_plot_calibrate.Rd
index 12e95ae8..8871146a 100644
--- a/man/cyto_plot_calibrate.Rd
+++ b/man/cyto_plot_calibrate.Rd
@@ -41,12 +41,14 @@ extract samples that should be used to calibrate the channels, set to NULL
 by default to calibrate channels using data from all samples.}
 
 \item{type}{indicates the type of calibration to perform, options include
-\code{"range"} or \code{"quantile"}, set to \code{"quantile"} by default.
-Range calibration simply uses the full range of values across samples for
-the calibration. Quantile calibration computes an lower and upper quantile
-for each channel, values falling outside the calibration range are assigned
-the bottom or top colour. Alternatively, users can also supply their own
-custom calibration function to \code{type} that accepts a matrix.}
+\code{"instrument"}, \code{"range"} or \code{"quantile"}, set to
+\code{"quantile"} by default. Instrument calibartion uses the full
+instrument range in each channel for calibration. Range calibration simply
+uses the full range of values across samples for the calibration. Quantile
+calibration computes an lower and upper quantile for each channel, values
+falling outside the calibration range are assigned the bottom or top
+colour. Alternatively, users can also supply their own custom calibration
+function to \code{type} that accepts a matrix.}
 
 \item{probs}{vector of lower and upper probabilities passed to
 \code{stats:quantile} to compute quantiles, set to \code{c(0.01, 0.99)} by