diff --git a/R/differential_fxns.R b/R/differential_fxns.R index a48b9f8..fe5c4f4 100644 --- a/R/differential_fxns.R +++ b/R/differential_fxns.R @@ -13,7 +13,7 @@ NULL #' @export #' @examples #' \dontrun{ -#' meta_df <- data.frame("ID" = c("P1", "P2"), "group" = c("A", "B"))} +#' meta_df <- data.frame("ID" = c("P1", "P2"), "group" = c("A", "B")) #' dom_ls <- list("P1" = dom1, "P2" = dom2) #' summarize_linkages( #' domino_results = dom_ls, subject_meta = meta_df, diff --git a/man/count_linkage.Rd b/man/count_linkage.Rd index 21852c0..ea83361 100644 --- a/man/count_linkage.Rd +++ b/man/count_linkage.Rd @@ -29,3 +29,10 @@ a data frame with columns for the unique linkage features and the counts of how \description{ Count occurrences of linkages across multiple domino results from a linkage summary } +\examples{ +\dontrun{ +count_linkage(linkage_summary = linkage_ls, cluster = "CD8_T_cell", + group.by = "group", linkage = "rec_lig") +} + +} diff --git a/man/create_domino.Rd b/man/create_domino.Rd index 574029e..659265f 100644 --- a/man/create_domino.Rd +++ b/man/create_domino.Rd @@ -63,14 +63,17 @@ domino object prepared for \code{\link[=build_domino]{build_domino()}}, which wi network. } \examples{ -pbmc_dom_tiny_all <- pbmc_dom_tiny <- create_domino(rl_map = domino2:::rl_map_tiny, - features = domino2:::auc_tiny, counts = domino2:::RNA_count_tiny, z_scores = domino2:::RNA_zscore_tiny, - clusters = domino2:::clusters_tiny, tf_targets = domino2:::regulon_list_tiny, use_clusters = FALSE, - use_complexes = FALSE, rec_min_thresh = 0.1, remove_rec_dropout = TRUE, +pbmc_dom_tiny_all <- pbmc_dom_tiny <- create_domino( + rl_map = domino2:::rl_map_tiny, features = domino2:::auc_tiny, + counts = domino2:::RNA_count_tiny, z_scores = domino2:::RNA_zscore_tiny, + clusters = domino2:::clusters_tiny, tf_targets = domino2:::regulon_list_tiny, + use_clusters = FALSE, use_complexes = FALSE, + rec_min_thresh = 0.1, remove_rec_dropout = TRUE, tf_selection_method = "all") -pbmc_dom_tiny_clustered <- create_domino(rl_map = domino2:::rl_map_tiny, - features = domino2:::auc_tiny, counts = domino2:::RNA_count_tiny, z_scores = domino2:::RNA_zscore_tiny, +pbmc_dom_tiny_clustered <- create_domino( + rl_map = domino2:::rl_map_tiny, features = domino2:::auc_tiny, + counts = domino2:::RNA_count_tiny, z_scores = domino2:::RNA_zscore_tiny, clusters = domino2:::clusters_tiny, tf_targets = domino2:::regulon_list_tiny, use_clusters = TRUE, use_complexes = TRUE, remove_rec_dropout = FALSE) diff --git a/man/feat_heatmap.Rd b/man/feat_heatmap.Rd index 0d76fdc..11cf3ae 100644 --- a/man/feat_heatmap.Rd +++ b/man/feat_heatmap.Rd @@ -52,6 +52,8 @@ activation scores) by cells organized by cluster. #basic usage feat_heatmap(domino2:::pbmc_dom_built_tiny) #using thresholds -feat_heatmap(domino2:::pbmc_dom_built_tiny, min_thresh = 0.1, max_thresh = 0.6, norm = TRUE, bool = FALSE) +feat_heatmap( + domino2:::pbmc_dom_built_tiny, min_thresh = 0.1, + max_thresh = 0.6, norm = TRUE, bool = FALSE) } diff --git a/man/gene_network.Rd b/man/gene_network.Rd index 6e8e90f..b252f1c 100644 --- a/man/gene_network.Rd +++ b/man/gene_network.Rd @@ -43,6 +43,8 @@ will be included in the plot. } \examples{ #basic usage -gene_network(domino2:::pbmc_dom_built_tiny, clust = "CD8_T_cell", OutgoingSignalingClust = "CD14_monocyte") +gene_network( + domino2:::pbmc_dom_built_tiny, clust = "CD8_T_cell", + OutgoingSignalingClust = "CD14_monocyte") } diff --git a/man/plot_differential_linkages.Rd b/man/plot_differential_linkages.Rd index d398904..05bec87 100644 --- a/man/plot_differential_linkages.Rd +++ b/man/plot_differential_linkages.Rd @@ -29,3 +29,13 @@ a Heatmap-class object of features ranked by test_statistic annotated with the p \description{ Plot differential linkages among domino results ranked by a comparative statistic } +\examples{ +\dontrun{ +plot_differential_linkages( + differential_linkages = diff_linkages_tiny, + test_statistic = "p.value", + stat_ranking = "ascending" +) +} + +} diff --git a/man/signaling_network.Rd b/man/signaling_network.Rd index aae503b..03db3a4 100644 --- a/man/signaling_network.Rd +++ b/man/signaling_network.Rd @@ -65,7 +65,9 @@ colored based on the color scheme of the ligand expressing cluster. #basic usage signaling_network(domino2:::pbmc_dom_built_tiny) # scaling, thresholds, layouts, selecting clusters -signaling_network(domino2:::pbmc_dom_built_tiny, showOutgoingSignalingClusts = "CD14_monocyte", scale = "none", - norm = "none", layout = "fr", scale_by = "none", vert_scale = 5) +signaling_network( + domino2:::pbmc_dom_built_tiny, showOutgoingSignalingClusts = "CD14_monocyte", + scale = "none", norm = "none", layout = "fr", scale_by = "none", + vert_scale = 5) } diff --git a/man/summarize_linkages.Rd b/man/summarize_linkages.Rd index 52dd6ae..fe2a7f3 100644 --- a/man/summarize_linkages.Rd +++ b/man/summarize_linkages.Rd @@ -19,3 +19,13 @@ A linkage summary class object consisting of nested lists of the active transcri \description{ Creates a linkage_summary object storing the linkages learned in different domino objects as nested lists to facilitate comparisons of networks learned by domino across subject covariates. } +\examples{ +\dontrun{ +meta_df <- data.frame("ID" = c("P1", "P2"), "group" = c("A", "B")) +dom_ls <- list("P1" = dom1, "P2" = dom2) +summarize_linkages( + domino_results = dom_ls, subject_meta = meta_df, + subject_names = meta_df$ID) +} + +} diff --git a/man/table_convert_genes.Rd b/man/table_convert_genes.Rd index 5736502..966e536 100644 --- a/man/table_convert_genes.Rd +++ b/man/table_convert_genes.Rd @@ -20,7 +20,7 @@ and rows corresponding to the gene symbols themselves} Data frame of genes with original and corresponding converted symbols } \description{ -Takes a vector of gene inputs and a conversion table (\href{"http://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt"}{an example} -and returns converted gene table +Takes a vector of gene inputs and a conversion table and returns a +converted gene table } \keyword{internal} diff --git a/man/test_differential_linkages.Rd b/man/test_differential_linkages.Rd index 4f41eb2..6d6e1a3 100644 --- a/man/test_differential_linkages.Rd +++ b/man/test_differential_linkages.Rd @@ -47,3 +47,10 @@ a data frame of results from the test of the differential linkages. Rows corresp \description{ Statistical test for differential linkages across multiple domino results } +\examples{ +\dontrun{ +test_differential_linkages(linkage_summary = linkage_ls, cluster = "CD8_T_cell", + group.by = "group", linkage = "rec_lig", test_name = "fishers.exact") +} + +}