Fix plot_bar_dendro in #22

Author: bschilder

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MSTExplorer
 Title: Multi-Scale Target Explorer
-Version: 1.0.6
+Version: 1.0.7
 Authors@R:
     c(
     person(given = "Brian",

MSTExplorer.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: d3448f8d-1b38-4b27-bcf0-25454d048582
 
 RestoreWorkspace: No
 SaveWorkspace: No

NAMESPACE

@@ -10,6 +10,7 @@ export(ewce_para)
 export(gen_overlap)
 export(gen_results)
 export(get_bg)
+export(get_cl)
 export(get_unfinished_list_names)
 export(ggnetwork_plot_full)
 export(load_example_ctd)

NEWS.md

@@ -1,10 +1,15 @@
 # MSTExplorer 1.0.7
 
+## New features
+* `get_cl`: new wrapper for getting the exact version of the 
+  Cell Ontology used in our original study.
+
 ## Bug fixes
-* M
+* Use `BiocMananger` to install in README.
+* `plot_bar_dendro`: Fix https://github.com/neurogenomics/MSTExplorer/issues/22
+* `plot_tissues`: Don't try to facet plot types that aren't requested.
 
 # MSTExplorer 1.0.6
-
 ## Bug fixes
 * `get_color_map`
   - Fix `color_vector` assignment.

R/fix_cl_ids.R

@@ -1,5 +1,5 @@
 fix_cl_ids <- function(dat,
-                       ont=KGExplorer::get_ontology("cl"),
+                       ont=get_cl(),
                        replace_map=list(
                          "CSH1_CSH2_positive_cells"="CL:0000351",
                          "SLC26A4_PAEP_positive_cells"="CL:0002097",

R/get_cl.R

@@ -0,0 +1,25 @@
+#' Get Cell Ontology
+#'
+#' A thin wrapper around \link[KGExplorer]{get_ontology} to get the
+#' specific version of the Cell Ontology used in the original analyses that
+#' produced the results stored in \link{load_example_results}.
+#'
+#' @inheritParams KGExplorer::get_ontology
+#' @inheritDotParams KGExplorer::get_ontology
+#' @export
+#' @examples
+#' cl <- get_cl()
+get_cl <- function(name = "cl",
+                   tag = "v2023-09-21",
+                   lvl = 1,
+                   remove_rings=TRUE,
+                   ...){
+  KGExplorer::get_ontology(name = name,
+                           tag = tag,
+                           lvl = lvl,
+                           remove_rings = remove_rings,
+                           ...) |>
+    KGExplorer::filter_ontology(
+      keep_descendants = "cell"
+    )
+}

R/get_target_celltypes.R

@@ -1,6 +1,5 @@
 get_target_celltypes <- function(target_branches = get_target_branches(),
-                                 cl = KGExplorer::get_ontology("cl",
-                                                               remove_rings=TRUE)
+                                 cl = get_cl()
                                  ){
   KGExplorer::get_ontology_descendants(ont = cl,
                                        terms = target_branches)

R/ontology_to_ggdendro.R

@@ -1,5 +1,4 @@
-ontology_to_ggdendro <- function(ont=KGExplorer::get_ontology(name = "cl",
-                                                              lvl = 1),
+ontology_to_ggdendro <- function(ont=get_cl(),
                                  terms=NULL #as.character(unique(results$cl_id))
                                  ){
   #### Get celltype dendrogram ####

R/order_celltypes.R

@@ -1,8 +1,5 @@
 order_celltypes <- function(dt,
-                            cl=KGExplorer::get_ontology("cl")|>
-                              KGExplorer::filter_ontology(
-                                keep_descendants = "cell"
-                              ),
+                            cl=get_cl(),
                             levels=NULL
                             ){
   cl_id <- cl_name <- NULL;

R/plot_bar_dendro.R

@@ -37,9 +37,7 @@ plot_bar_dendro <- function(results = load_example_results(),
                             target_branches = get_target_branches(),
                             keep_ancestors=names(target_branches),
                             hpo = HPOExplorer::get_hpo(),
-                            cl = KGExplorer::get_ontology(name = "cl",
-                                                          lvl = 1,
-                                                          remove_rings = TRUE),
+                            cl = get_cl(),
                             facets = "ancestor_name",
                             add_test_target_celltypes=TRUE,
                             add_prop_test=FALSE,
@@ -116,6 +114,7 @@ plot_bar_dendro <- function(results = load_example_results(),
   tissue_plots <- plot_tissues(results = results,
                                facet_var = "dummy",
                                types = "bar")
+
   ggsummary <- tissue_plots$bar_plot +
                   ggplot2::labs(x=NULL, y=NULL) +
                   ggplot2::scale_fill_gradient(low="black",high="grey") +