reversion to dontrun

Without prepared data objects in sysdata.rda, donttest examples produce an error. dontrun code will be kept in place until the test data is implemented.

R/differential_fxns.R

@@ -12,7 +12,7 @@ NULL
 #' @return A linkage summary class object consisting of nested lists of the active transcription factors, active receptors, and incoming ligands for each cluster across multiple domino results.
 #' @export
 #' @examples 
-#' \donttest{
+#' \dontrun{
 #' meta_df <- data.frame("ID" = c("P1", "P2"), "group" = c("A", "B"))
 #' dom_ls <- list("P1" = dom1, "P2" = dom2)
 #' summarize_linkages(
@@ -108,7 +108,7 @@ summarize_linkages <- function(domino_results, subject_meta, subject_names = NUL
 #' @return a data frame with columns for the unique linkage features and the counts of how many times the linkage occured across the compared domino results. If group.by is used, counts of the linkages are also provided as columns named by the unique values of the group.by variable.
 #' @export
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' count_linkage(linkage_summary = linkage_ls, cluster = "CD8_T_cell", 
 #'  group.by = "group", linkage = "rec_lig")
 #' }
@@ -170,7 +170,7 @@ count_linkage <- function(linkage_summary, cluster, group.by = NULL, linkage = "
 #' }
 #' @export
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' test_differential_linkages(linkage_summary = linkage_ls, cluster = "CD8_T_cell", 
 #'  group.by = "group", linkage = "rec_lig", test_name = "fishers.exact")
 #' }

R/plot_fxns.R

@@ -870,7 +870,7 @@ circos_ligand_receptor <- function(
 #' @return a Heatmap-class object of features ranked by test_statistic annotated with the proportion of subjects that showed active linkage of the features.
 #' @export
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' plot_differential_linkages(
 #'  differential_linkages = diff_linkages_tiny,
 #'  test_statistic = "p.value",

R/processing_fxns.R

@@ -13,8 +13,10 @@
 #' @return A domino object with a signaling network built
 #' @export
 #' @examples
-#' pbmc_dom_tiny_built <- build_domino(dom = domino2:::pbmc_dom_tiny, min_tf_pval = .001, max_tf_per_clust = 25,
-#'  max_rec_per_tf = 25, rec_tf_cor_threshold = .25, min_rec_percentage = 0.1)
+#' pbmc_dom_tiny_built <- build_domino(
+#'  dom = domino2:::pbmc_dom_tiny, min_tf_pval = .001, max_tf_per_clust = 25,
+#'  max_rec_per_tf = 25, rec_tf_cor_threshold = .25, min_rec_percentage = 0.1
+#' )
 #' 
 build_domino <- function(
     dom, max_tf_per_clust = 5, min_tf_pval = 0.01, max_rec_per_tf = 5, rec_tf_cor_threshold = 0.15,