From 42d1f589ac6291449551d9ef92186446355b7d85 Mon Sep 17 00:00:00 2001
From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com>
Date: Thu, 22 Aug 2024 00:42:22 +0100
Subject: [PATCH] Fix plot_upheno

---
 R/plot_upheno.R         |  7 +++++--
 R/plot_upheno_heatmap.R | 40 +++++++++++++++++++++-------------------
 man/plot_.Rd            |  3 ++-
 man/plot_upheno.Rd      |  5 ++++-
 4 files changed, 32 insertions(+), 23 deletions(-)

diff --git a/R/plot_upheno.R b/R/plot_upheno.R
index a7bc4c5..c45dae1 100644
--- a/R/plot_upheno.R
+++ b/R/plot_upheno.R
@@ -8,6 +8,7 @@
 #' @param pheno_map_genes_match uPheno cross-species mapping data generated by
 #' \link[KGExplorer]{map_upheno_data}.
 #' \code{pheno_map_genes_match} by.
+#' @param ... Arguments passed to plotting functions.
 #' @returns A named list of \pkg{ggplot2} objects.
 #'
 #' @export
@@ -20,7 +21,8 @@
 plot_upheno <- function(pheno_map_genes_match=NULL,
                         filters=list(db1="HP",
                                      gene_taxon_label1="Homo sapiens"),
-                        types=c("rainplot","scatterplot","heatmap")){
+                        types=c("rainplot","scatterplot","heatmap"),
+                        ...){
   ## Prepare plot data
   id1 <- n_phenotypes <-NULL;
   {
@@ -47,7 +49,8 @@ plot_upheno <- function(pheno_map_genes_match=NULL,
     plots[["scatterplot"]] <- plot_upheno_scatterplot(plot_dat = plot_dat)
   }
   if("heatmap" %in% types){
-    plots[["heatmap"]] <- plot_upheno_heatmap(plot_dat = plot_dat)
+    plots[["heatmap"]] <- plot_upheno_heatmap(plot_dat = plot_dat,
+                                              ...)
   }
   return(plots)
 }
diff --git a/R/plot_upheno_heatmap.R b/R/plot_upheno_heatmap.R
index 58918c2..55a2be4 100644
--- a/R/plot_upheno_heatmap.R
+++ b/R/plot_upheno_heatmap.R
@@ -1,18 +1,19 @@
 #' @describeIn plot_ plot_
 plot_upheno_heatmap <- function(plot_dat,
-                               ont=get_ontology("upheno",
-                                                add_ancestors = 10),
-                               hpo_ids=NULL,
-                               value.var=c("phenotype_genotype_score",
-                                           "prop_intersect",
-                                           "equivalence_score",
-                                           "subclass_score"),
-                               name=value.var[1],
-                               min_rowsums=NULL,
-                               cluster_from_ontology=FALSE,
-                               save_dir=tempdir(),
-                               height = 15,
-                               width = 10){
+                                lvl=10,
+                                 ont=get_ontology("upheno",
+                                                  lvl = lvl),
+                                 hpo_ids=NULL,
+                                 value.var=c("phenotype_genotype_score",
+                                             "prop_intersect",
+                                             "equivalence_score",
+                                             "subclass_score"),
+                                 name=value.var[1],
+                                 min_rowsums=NULL,
+                                 cluster_from_ontology=FALSE,
+                                 save_dir=tempdir(),
+                                 height = 15,
+                                 width = 10){
   requireNamespace("ComplexHeatmap")
   hpo_id <- object_label1 <- NULL;
   set.seed(2023)
@@ -25,7 +26,7 @@ plot_upheno_heatmap <- function(plot_dat,
   plot_dat[,hpo_id:=id1][,object_label1:=gsub(" (HPO)","",
                                               object_label1,fixed = TRUE)]
   if(isFALSE(cluster_from_ontology)){
-    ont <- add_ancestors(ont)
+    ont <- add_ancestors(ont, lvl = lvl)
     if(!"ancestor_name" %in% names(plot_dat)){
       plot_dat <- merge(
         plot_dat,
@@ -88,13 +89,14 @@ plot_upheno_heatmap <- function(plot_dat,
   #       max(annot_dat$n_genes_db1),
   #       length.out=4),
   #   pals::gnuplot(4))
+  data.table::setnames(annot_dat,"n_genes_db1","N genes (HPO)")
   la <- ComplexHeatmap::rowAnnotation(
     df=data.frame(annot_dat[,-c("object_label1")],
-                  row.names = annot_dat$label1),
-    # ?ComplexHeatmap::Legend
-    show_legend = c(TRUE, FALSE),
-    annotation_legend_param = list(
-      n_genes_db1= list(title = "HPO genes"))
+                  row.names = annot_dat$object_label1, 
+                  check.names = FALSE),
+    show_legend = c(TRUE, FALSE)
+    # annotation_legend_param = list(
+    #   `N genes (HPO)`= list(title = "HPO genes"))
   )
   row_split <- if(isFALSE(cluster_from_ontology)) annot_dat$ancestor_name
   #### make heatmap ####
diff --git a/man/plot_.Rd b/man/plot_.Rd
index 0fe1774..d5a6c38 100644
--- a/man/plot_.Rd
+++ b/man/plot_.Rd
@@ -122,7 +122,8 @@ plot_save(plt, save_path = save_path, width = NULL, height = width)
 
 plot_upheno_heatmap(
   plot_dat,
-  ont = get_ontology("upheno", add_ancestors = 10),
+  lvl = 10,
+  ont = get_ontology("upheno", lvl = lvl),
   hpo_ids = NULL,
   value.var = c("phenotype_genotype_score", "prop_intersect", "equivalence_score",
     "subclass_score"),
diff --git a/man/plot_upheno.Rd b/man/plot_upheno.Rd
index 4fad79f..8c7b7e7 100644
--- a/man/plot_upheno.Rd
+++ b/man/plot_upheno.Rd
@@ -7,7 +7,8 @@
 plot_upheno(
   pheno_map_genes_match = NULL,
   filters = list(db1 = "HP", gene_taxon_label1 = "Homo sapiens"),
-  types = c("rainplot", "scatterplot", "heatmap")
+  types = c("rainplot", "scatterplot", "heatmap"),
+  ...
 )
 }
 \arguments{
@@ -20,6 +21,8 @@ a column in the data, and the vector within each element represents the
 values to include in the final data.}
 
 \item{types}{A character vector of plot types to generate.}
+
+\item{...}{Arguments passed to plotting functions.}
 }
 \value{
 A named list of \pkg{ggplot2} objects.