From 8ed7100f2b914a3e4aab34224cb79ef4c9f1115f Mon Sep 17 00:00:00 2001
From: Stevie Ped <stephen.pederson.au@gmail.com>
Date: Fri, 29 Sep 2023 23:55:04 +0930
Subject: [PATCH] Added respectLevels to plotProfileHeatmap

---
 R/fitAssayDiff.R                  | 2 +-
 R/plotProfileHeatmap.R            | 7 +++++--
 man/fitAssayDiff-methods.Rd       | 2 +-
 man/plotProfileHeatmap-methods.Rd | 5 +++++
 4 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/R/fitAssayDiff.R b/R/fitAssayDiff.R
index dc289821..b7d45c89 100644
--- a/R/fitAssayDiff.R
+++ b/R/fitAssayDiff.R
@@ -43,7 +43,7 @@
 #' integrating multiple ChIP targets due to the increase in false-negatives when
 #' using a range-based H0, and when requiring more accurate identification of
 #' truly unchanged sites, as opposed to those which simply fail to achieve
-#' significance using a range-based H0.
+#' significance using a range-based H0 where arbitrary cutoff values are used.
 #'
 #' @param x a SummarizedExperiment object
 #' @param assay The assay to use for analysis
diff --git a/R/plotProfileHeatmap.R b/R/plotProfileHeatmap.R
index b517221e..0db96ab9 100644
--- a/R/plotProfileHeatmap.R
+++ b/R/plotProfileHeatmap.R
@@ -43,6 +43,9 @@
 #' Represents the fraction of the plotting area taken up by the summary panel.
 #' @param summaryLabelSide Side to place y-axis for the summary plot in the top
 #' panel
+#' @param respectLevels logical(1) If FALSE, facets along the y-axis will be
+#' arranged in descending order of signal, otherwise any original factor levels
+#' will be retained
 #' @param ... Passed to \link[ggplot2]{facet_grid} internally. Can be utilised
 #' for switching panel strips or passing a labeller function
 #'
@@ -140,7 +143,7 @@ setMethod(
         facetX = NULL, facetY = NULL, colour = facetY, linetype = NULL,
         summariseBy = c("mean", "median", "min", "max", "none"),
         xLab = xValue, yLab = NULL, fillLab = fillValue, relHeight = 0.3,
-        summaryLabelSide = "left", ...
+        summaryLabelSide = "left", respectLevels = FALSE, ...
     ) {
 
         ## Check the profile data.frames for identical dims & required cols
@@ -171,7 +174,7 @@ setMethod(
         tbl <- arrange(tbl, desc(!!sym(fillValue)))
         ## Ensure the ranges are shown with the strongest signal at the top
         tbl$range <- fct_rev(fct_inorder(tbl$range))
-        if (!is.null(facetY))
+        if (!is.null(facetY) & !respectLevels)
             tbl[[facetY]] <- fct_inorder(as.character(tbl[[facetY]]))
 
         ## Pass to the private function
diff --git a/man/fitAssayDiff-methods.Rd b/man/fitAssayDiff-methods.Rd
index 818da19b..218c9889 100644
--- a/man/fitAssayDiff-methods.Rd
+++ b/man/fitAssayDiff-methods.Rd
@@ -84,7 +84,7 @@ These are not used for FDR-adjusted p-values but can be helpful when
 integrating multiple ChIP targets due to the increase in false-negatives when
 using a range-based H0, and when requiring more accurate identification of
 truly unchanged sites, as opposed to those which simply fail to achieve
-significance using a range-based H0.
+significance using a range-based H0 where arbitrary cutoff values are used.
 }
 \description{
 Detect differential ChIP signal using one of many approaches
diff --git a/man/plotProfileHeatmap-methods.Rd b/man/plotProfileHeatmap-methods.Rd
index 593bb951..fa235174 100644
--- a/man/plotProfileHeatmap-methods.Rd
+++ b/man/plotProfileHeatmap-methods.Rd
@@ -40,6 +40,7 @@ plotProfileHeatmap(object, ...)
   fillLab = fillValue,
   relHeight = 0.3,
   summaryLabelSide = "left",
+  respectLevels = FALSE,
   ...
 )
 }
@@ -73,6 +74,10 @@ Represents the fraction of the plotting area taken up by the summary panel.}
 
 \item{summaryLabelSide}{Side to place y-axis for the summary plot in the top
 panel}
+
+\item{respectLevels}{logical(1) If FALSE, facets along the y-axis will be
+arranged in descending order of signal, otherwise any original factor levels
+will be retained}
 }
 \value{
 A \code{ggplot2} object, able to be customised using standard \code{ggplot2} syntax