Scdrake spatial

NAMESPACE

@@ -4,6 +4,7 @@ S3method("$",scdrake_list)
 S3method("[",scdrake_list)
 S3method("[[",scdrake_list)
 export("%&&%")
+export(LR_data_fn)
 export(SCDRAKE_CLI_VERSION)
 export(add_item_to_list)
 export(add_marker_table_links)
@@ -14,6 +15,8 @@ export(calc_sc3)
 export(catg0)
 export(catn)
 export(cc_genes_fn)
+export(cellProximityBarplot_fn)
+export(cellProximityHeatmap_fn)
 export(cell_annotation_diagnostic_plots_files_fn)
 export(cell_annotation_diagnostic_plots_fn)
 export(cell_annotation_fn)
@@ -50,11 +53,13 @@ export(contrasts_heatmaps_df_fn)
 export(contrasts_out_fn)
 export(contrasts_params_fn)
 export(contrasts_plot_params_fn)
+export(createGiotto_fn)
 export(create_a_link)
 export(create_dummy_plot)
 export(create_img_link)
 export(create_integration_dirs)
 export(create_seu_for_heatmaps)
+export(create_signature_matrix_fn)
 export(create_single_sample_dirs)
 export(dimred_plots_cell_annotation_params_df_fn)
 export(dimred_plots_clustering_fn)
@@ -75,6 +80,7 @@ export(generate_dimred_plots_clustering_section)
 export(generate_dimred_plots_section)
 export(generate_markers_results_section)
 export(generate_stage_report)
+export(getDistinctColors)
 export(get_cell_annotation_subplan)
 export(get_cluster_markers_subplan)
 export(get_clustering_graph_subplan)
@@ -137,8 +143,11 @@ export(markers_plots_top)
 export(markers_table_files)
 export(md_header)
 export(merge_sce_metadata)
+export(meta_heatmap_ploting)
 export(na_empty)
 export(pca_phase_plots_fn)
+export(plotCCcomDotplot_fn)
+export(plotCCcomHeatmap_fn)
 export(plotReducedDim_mod)
 export(plot_clustree)
 export(plot_colData)
@@ -152,6 +161,7 @@ export(run_graph_based_clustering)
 export(run_integration)
 export(run_integration_r)
 export(run_kmeans_clustering)
+export(run_page_man_annotation)
 export(run_single_sample)
 export(run_single_sample_r)
 export(save_clustree)
@@ -197,6 +207,7 @@ export(selected_markers_int_plots_df_fn)
 export(selected_markers_plots_fn)
 export(set_rstudio_drake_cache)
 export(seu_add_metadata)
+export(spatGenePlot2Dsce)
 export(str_comma)
 export(str_line)
 export(str_space)
@@ -206,6 +217,7 @@ export(update_integration_configs)
 export(update_pipeline_config)
 export(update_project)
 export(update_single_sample_configs)
+export(visualized_spots)
 export(which_genes_regex)
 export(with_dbi)
 export(with_plan)

R/hvg.R

@@ -1,5 +1,5 @@
 ## -- Common functions related to highly variable genes (HVGs) selection.
-
+##here comes some changes
 #' @title Get top N highly variable genes (HVGs) by a specified metric.
 #' @description Types of HVG metrics are specified in `02_norm_clustering.yaml` and `01_integration.yaml` configs.
 #' See the corresponding section there.