From 65a6f539d1bb2de5e5545712f3fe18c6f65028dc Mon Sep 17 00:00:00 2001
From: Chirag Parsania <chirag.parsania@gmail.com>
Date: Wed, 31 Jul 2024 12:38:38 +1000
Subject: [PATCH] argument row_order removed

---
 R/chip_related.R                               | 13 ++-----------
 docs/reference/make_enriched_heatmap_list.html |  5 -----
 man/make_enriched_heatmap_list.Rd              |  3 ---
 3 files changed, 2 insertions(+), 19 deletions(-)

diff --git a/R/chip_related.R b/R/chip_related.R
index cb56270..ec71e95 100644
--- a/R/chip_related.R
+++ b/R/chip_related.R
@@ -288,7 +288,6 @@ import_topn_bed_features <- function(bed_feature_file,topn = 5000, center = TRUE
 #' @param heatmap_axis_name_rot internally passed to \code{axis_name_rot} argument of [EnrichedHeatmap::EnrichedHeatmap()].
 #' @param heatmap_axis_name_gp internally passed to \code{axis_name_gp} argument of [EnrichedHeatmap::EnrichedHeatmap()].
 #' @param heatmap_border internally passed to \code{border} argument of [EnrichedHeatmap::EnrichedHeatmap()].
-#' @param row_order internally passed to \code{row_order} argument of [EnrichedHeatmap::EnrichedHeatmap()].
 #'
 #' @return a HeatmapList.
 #' @export
@@ -298,7 +297,6 @@ import_topn_bed_features <- function(bed_feature_file,topn = 5000, center = TRUE
 #' }
 #'
 make_enriched_heatmap_list <- function(x,
-                                       row_order = NULL,
                                        cluster_targets_by_rpm = TRUE,
                                        cluster_by = NULL,
                                        n_clust = 2,
@@ -401,9 +399,7 @@ make_enriched_heatmap_list <- function(x,
                                                                             pos_line = heatmap_pos_line,
                                                                             pos_line_gp = heatmap_pos_line_gp,
                                                                             axis_name_rot = heatmap_axis_name_rot,
-                                                                            border = heatmap_border,
-                                                                            row_order = ifelse(is.null(row_order),
-                                                                                               order(enriched_score(assays(x)[[..1]]), decreasing = TRUE), row_order)))
+                                                                            border = heatmap_border))
 
 
 
@@ -430,13 +426,8 @@ make_enriched_heatmap_list <- function(x,
   }
 
   # if row_order NULL then split by clusters , else default row order
-  if(is.null(row_order)){
-    hm_list_draw <- ComplexHeatmap::draw(hm_list, split = peak_clust$clust)
-  } else {
-    hm_list_draw <- ComplexHeatmap::draw(hm_list)
-  }
-
 
+    hm_list_draw <- ComplexHeatmap::draw(hm_list, split = peak_clust$clust)
 
   return(hm_list_draw)
 
diff --git a/docs/reference/make_enriched_heatmap_list.html b/docs/reference/make_enriched_heatmap_list.html
index 547e01f..8f32da4 100644
--- a/docs/reference/make_enriched_heatmap_list.html
+++ b/docs/reference/make_enriched_heatmap_list.html
@@ -50,7 +50,6 @@
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">make_enriched_heatmap_list</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
-<span>  row_order <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  cluster_targets_by_rpm <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  cluster_by <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  n_clust <span class="op">=</span> <span class="fl">2</span>,</span>
@@ -75,10 +74,6 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dd><p>an object of the class parcutils_chip.</p></dd>
 
 
-<dt>row_order</dt>
-<dd><p>internally passed to <code>row_order</code> argument of <code><a href="https://rdrr.io/pkg/EnrichedHeatmap/man/EnrichedHeatmap.html" class="external-link">EnrichedHeatmap::EnrichedHeatmap()</a></code>.</p></dd>
-
-
 <dt>cluster_targets_by_rpm</dt>
 <dd><p>logical, denoting weather to cluster targets by RPM value.</p></dd>
 
diff --git a/man/make_enriched_heatmap_list.Rd b/man/make_enriched_heatmap_list.Rd
index e1c30dd..9f2ebd8 100644
--- a/man/make_enriched_heatmap_list.Rd
+++ b/man/make_enriched_heatmap_list.Rd
@@ -6,7 +6,6 @@
 \usage{
 make_enriched_heatmap_list(
   x,
-  row_order = NULL,
   cluster_targets_by_rpm = TRUE,
   cluster_by = NULL,
   n_clust = 2,
@@ -27,8 +26,6 @@ make_enriched_heatmap_list(
 \arguments{
 \item{x}{an object of the class parcutils_chip.}
 
-\item{row_order}{internally passed to \code{row_order} argument of \code{\link[EnrichedHeatmap:EnrichedHeatmap]{EnrichedHeatmap::EnrichedHeatmap()}}.}
-
 \item{cluster_targets_by_rpm}{logical, denoting weather to cluster targets by RPM value.}
 
 \item{cluster_by}{NULL (default) or character vector denoting RPM columns to be used for clustering.}