Fix plot_bar_dendro_facets

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MSTExplorer
 Title: Multi-Scale Target Explorer
-Version: 1.0.0
+Version: 1.0.1
 Authors@R:
     c(
     person(given = "Brian",

NEWS.md

@@ -1,3 +1,11 @@
+# MSTExplorer 1.0.1
+
+## Bug fixes
+
+* `plot_bar_dendro_facets`
+  - Add `hpo` arg to pass HPO directly.
+  - Fix `data_summary` so that denominator is the number of on-target cell types only.
+
 # MSTExplorer 1.0.0
 
 ## New features

R/add_logfc.R

@@ -16,8 +16,8 @@ add_logfc <- function(results,
     messager("Adding logFC column.")
     # results[,logFC:=log10(scales::rescale(estimate,c(.Machine$double.xmin, 1)))]
     # results[,logFC:=logFC/mean(results$logFC)]
-    results[,logFC:=get(effect_var)+abs(min(get(effect_var)))]
-    results[,logFC:=log2(logFC/mean(results$logFC))]
+    results[,logFC:=(get(effect_var)+abs(min(get(effect_var))))]
+    results[,logFC:=(log2(logFC/mean(results$logFC)))]
     # hist(results$logFC)
   } else {
     messager("logFC already exists in results.",

R/plot_bar_dendro.R

@@ -16,6 +16,8 @@
 #' denoted by "*" above its bar.
 #' @param expand_dendro_x Passed to \link[ggplot2]{scale_x_discrete}
 #' in the cell type dendrogram.
+#' @param cl Cell Ontology (CL) object from
+#'  \code{KGExplorer::get_ontology("cl")}.
 #' @inheritParams plot_
 #' @inheritParams ggnetwork_plot_full
 #' @inheritParams HPOExplorer::add_ancestor
@@ -133,7 +135,8 @@ plot_bar_dendro <- function(results = load_example_results(),
                                   color_vector=color_vector,
                                   legend.position=legend.position,
                                   q_threshold=q_threshold,
-                                  facets=facets)
+                                  facets=facets,
+                                  hpo=hpo)
   ggbars <- ggbars_out$plot
   #### Create dendrogram plot ####
   ggdend <-

R/plot_bar_dendro_facets.R

@@ -49,6 +49,7 @@
 #'                          background_full=FALSE)
 plot_bar_dendro_facets <- function(results = load_example_results(),
                                   results_full = NULL,
+                                  hpo=HPOExplorer::get_hpo(),
                                   target_branches = get_target_branches(),
                                   keep_ancestors = names(target_branches),
                                   target_celltypes = get_target_celltypes(
@@ -98,25 +99,29 @@ plot_bar_dendro_facets <- function(results = load_example_results(),
     }
     results <- HPOExplorer::add_ancestor(results,
                                          lvl = lvl,
+                                         hpo=hpo,
                                          force_new = TRUE)
     results[, phenotypes_per_ancestor:=data.table::uniqueN(hpo_id),
             by=c("ancestor","ancestor_name")]
   }
   if("hpo_name" %in% c(fill_var,facets)){
-    results <- HPOExplorer::add_hpo_name(results)
+    results <- HPOExplorer::add_hpo_name(results,
+                                         hpo=hpo)
   }
   #### Create filtered dataset for plotting ####
   {
     if(!is.null(keep_ancestors) &&
        "hpo_name" %in% names(results)){
       dat <- HPOExplorer::filter_descendants(phenos = results,
+                                             hpo = hpo,
                                              keep_descendants = keep_ancestors)
     } else {
       dat <- data.table::copy(results)
     }
     if(nrow(dat)==0) stopper("0 associations remaining.")
     if(!is.null(keep_ont_levels) || "ontLvl" %in% c(facets,cols)){
       dat <- HPOExplorer::add_ont_lvl(dat,
+                                      hpo=hpo,
                                       keep_ont_levels = keep_ont_levels)
     }
     if(!is.null(target_branches_keep)){
@@ -172,8 +177,8 @@ plot_bar_dendro_facets <- function(results = load_example_results(),
       data_summary <- dat[,list(
         target_celltypes=paste(target_branches[[ancestor_name]],collapse = "/"),
         phenotypes_per_ancestor=unique(phenotypes_per_ancestor),
-        n_celltypes=data.table::uniqueN(cl_name),
-        n_celltypes_sig=data.table::uniqueN(cl_name[p.value.adj<0.05])
+        n_celltypes=data.table::uniqueN(cl_name[term=="is_targetTRUE"]),
+        n_celltypes_sig=data.table::uniqueN(cl_name[term=="is_targetTRUE" & p.value.adj<0.05])
       ),
       by=c("ancestor_name")]
     }