R/zzz.R
In tanaylab/MCView: A Shiny App for Metacell Analysis
globalVariables(unique(c(
# add_gene_modules:
"gene", "module",
# add_genes_to_gene_module:
"gene",
# add_markers_colorbars:
"metacell",
# app_server:
"cell_type", "color", "config", "module", "project", "tab_defs",
# app_server : dataset:
"project",
# app_ui:
"project", "tab_defs",
# atlas_gene_gene:
"default_gene1", "default_gene2", "egc_epsilon",
# calc_ct_ct_gene_df:
"egc_epsilon",
# calc_gene_modules:
"clust", "gene", "module",
# calc_gg_mc_top_cor:
"col1", "col2", "val",
# calc_mc_mc_gene_df:
"egc_epsilon",
# calc_obs_exp_mc_df:
"egc_epsilon",
# calc_obs_exp_type_df:
"egc_epsilon",
# calc_samp_mc_count:
"mc_data", "metacell", "samp_id",
# calc_samp_mc_frac:
"mc_data",
# calc_samp_metadata:
"mc_data", "samp_id",
# calc_samp_samp_gene_df:
"egc_epsilon",
# calc_samples_list:
"mc_data",
# cell_metadata_to_metacell:
"cat_var_n", "cat_varp", "cell_id", "metacell",
# cell_metadata_to_metacell_from_h5ad:
"cell_id", "metacell_name", "outlier",
# cell_type_gene_boxplot:
"Cell type", "cell_type", "egc_epsilon", "expr_breaks", "metacell",
# cell_type_metadata_boxplot:
"Cell type", "cell_type", "metacell",
# cell_type_metadata_confusion:
"# of metacells", "% of cell type metacells", "Cell type", "cell_type", "color", "metacell", "n_tot", "n_tot_md", "p_cell_type", "p_md", "total # of cell type metacells",
# choose_markers:
"fp", "gene", "metacell",
# clipboard_reactives:
"cell_type", "metacell",
# clipboard_reactives : <anonymous>:
"cell_type", "metacell",
# colored_metacell_selector:
"config",
# compute_umap:
"idx", "k", "mc1", "mc2", "weight",
# config_shiny_cache:
"config", "project",
# download_modal_reactives : <anonymous>:
"project",
# dt_selector_column:
"cell_type",
# filter_mat_by_cell_types:
"cell_type", "metacell",
# fitted_genes_per_cell_type_plot:
"cell_type", "color", "type",
# fitted_genes_per_cell_type_table:
"common", "fitted_gene_of", "gene", "type",
# gene_correction_factor_scatter_plot:
"Correction factor", "correction_factor", "gene", "Gene", "Max expression", "max_expr", "type", "Type",
# gene_correction_factor_table:
"correction_factor", "gene", "Max expression", "max_expr", "type",
# gene_inner_fold_scatter_plot:
"# of metacells", "gene", "Gene", "Max expression", "max_expr", "significant_inner_folds_count", "type", "Type",
# gene_inner_fold_table:
"# of metacells", "gene", "Max expression", "max_expr", "significant_inner_folds_count", "type",
# gene_label:
"gene", "module",
# get_cell_type_colors:
"cell_type", "color",
# get_cell_type_data:
"cell_type", "mc_data",
# get_cell_types_mat:
"cell_type", "metacell",
# get_marker_genes:
"config",
# get_markers:
"cache_dir",
# get_mc_color_key:
"cell_type", "mc_col",
# get_mc_config:
"config",
# get_mc_data:
"mc_data",
# get_mc_gene_modules_egc:
"module",
# get_metacell_types_data:
"cell_type", "color", "mc_data", "metacell",
# get_metadata:
"mc_data",
# get_module_genes:
"gene",
# get_samples_egc:
"cell_type", "metacell",
# get_samples_mat:
"cell_type", "metacell",
# get_top_cor_gene:
"egc_epsilon", "gene1", "gene2", "label",
# golem_add_external_resources:
"config",
# group_selectors:
"cell_type", "metacell",
# group_selectors_mod_query:
"cell_type", "metacell",
# has_atlas:
"mc_data",
# heatmap_matrix_reactives:
"cell_type", "config", "metacell",
# heatmap_reactives : <anonymous>:
"cell_type", "color", "type",
# heatmap_sidebar:
"config",
# help_reactives:
"config", "help_config",
# import_atlas:
"atlas", "cell_type", "color", "dtype", "gene", "metacell", "projected_type", "similar", "top1_gene", "top1_lfp", "top2_gene", "top2_lfp", "type", "value", "weight",
# import_cell_metadata:
"cell_id", "metacell", "samp_id",
# import_dataset:
"cell_type", "cluster", "color", "correction_factor", "fp", "gene", "gene1", "gene2", "grouped", "metacell", "significant_inner_folds_count", "total_umis",
# import_dataset_metacell1:
"cell_type", "color", "metacell", "time_bin",
# init_config:
"config",
# init_selected_genes:
"config", "project",
# init_tab_defs:
"config", "tab_defs",
# init_temp_scdb:
".",
# initial_proj_point_size:
"config",
# initial_proj_stroke:
"config",
# initial_scatters_point_size:
"config",
# initial_scatters_stroke:
"config",
# layout_and_graph_to_mc2d:
"from", "metacell", "to",
# load_all_data:
"project",
# load_all_mc_data:
".", "mc_data",
# load_all_mc_data_atlas:
".", "mc_data",
# load_default_2d_projection:
"i", "j", "x", "y",
# load_outliers:
"fp",
# mc2d_plot_gene_ggp:
"cell_type", "egc_epsilon", "enrich", "expr_clipped", "mc_age", "metacell",
# mc2d_plot_metadata_ggp:
"Cell type", "cell_type", "mc_age", "mc_col", "metacell", "top1_gene", "top1_lfp", "top2_gene", "top2_lfp",
# mc2d_to_graph_df:
"d", "dx", "dy", "from", "mc1", "mc2", "metacell", "range_x", "range_y", "to", "weight", "x", "x_mc1", "x_mc2", "y", "y_mc1", "y_mc2",
# mc_mc_gene_scatter_df_reactive:
"cell_type", "metacell",
# mctnetwork_g_t_types:
"flow", "g_src", "g_targ", "mc_t1", "mc_t2", "src_g", "targ_g", "time1", "time2", "type1", "type2",
# metacell_colors_reactive:
"mc_col", "metacell",
# metacell_from_coords_proj:
"diff1", "diff2",
# metacell_selector:
"config",
# metacell_selectors:
"config",
# metacell_selectors_mod_query:
"cell_type", "config",
# metacells_to_types:
"cell_type", "metacell",
# min_edge_length:
"config",
# mod_about_server : <anonymous>:
"cell_type", "color", "default_gene1", "default_gene2", "x", "x_mc1", "x_mc2", "y", "y_mc1", "y_mc2",
# mod_about_ui:
"about_file", "config",
# mod_annotate_server : <anonymous>:
"color", "metacell", "project",
# mod_annotate_server : <anonymous> : <anonymous>:
"color", "metacell", "top1_gene", "top1_lfp", "top2_gene", "top2_lfp",
# mod_atlas_server : <anonymous>:
"project",
# mod_cell_type_server : <anonymous>:
"default_gene1", "egc_epsilon",
# mod_flow_server : <anonymous>:
"cell_type", "color", "default_gene1", "metacell",
# mod_gene_module_controllers:
"gene", "module",
# mod_gene_module_controllers : <anonymous>:
"gene", "module",
# mod_manifold_server : <anonymous>:
"mc1", "mc2", "project",
# mod_manifold_server : <anonymous> : <anonymous>:
"mc1", "mc2",
# mod_outliers_server : <anonymous>:
"cell_id", "metacell", "most_similar",
# mod_projection_qc_server : <anonymous>:
"fitted_gene_any", "gene", "marker_gene",
# mod_query_server : <anonymous>:
"cell_type", "default_gene1", "fitted_gene", "fitted_gene_any", "marker_gene", "metacell",
# mod_samples_server : <anonymous>:
"default_gene1", "default_gene2", "samp_id",
# modify_gene_names:
"alt_name", "gene_name", "new_name",
# observe_mc_click_event:
"cell_type", "metacell",
# observer_mc_select_event:
"cell_type", "metacell",
# order_mc_by_most_var_genes:
".", "cell_type", "ct_ord", "glob_ord", "metacell", "orig_ord", "rand",
# parse_cell_type_colors:
"cell_type", "cluster", "color",
# parse_metacell_types:
"age", "cluster", "metacell",
# parse_metadata:
"metacell",
# plot_gene_time_over_mc:
"Age", "Cell type", "cell_type", "egc_epsilon", "expr_breaks", "mc_age", "metacell", "Metacell",
# plot_gene_trajectory:
"egc_epsilon", "expr_breaks", "gene", "Gene", "time_bin", "time_desc",
# plot_gg_over_mc:
"Cell type", "cell_type", "egc_epsilon", "expr_breaks", "mc_age", "metacell", "Metacell",
# plot_markers_mat:
"cell_type", "color",
# plot_mc_mc_gene:
"expr_breaks", "gene", "Gene", "pval",
# plot_mc_scatter:
"cell_type", "color", "color_values", "egc_epsilon", "expr_breaks", "metacell", "Metacell",
# plot_mc_time_dist:
"Metacell age (E[t])", "n_cells", "time_bin", "time_desc",
# plot_obs_proj_scatter:
"cell_type", "color", "color_values", "egc_epsilon", "expr_breaks", "metacell", "Metacell", "query", "weight",
# plot_propagation_net_metacell:
"cell_type", "cell_type1", "edge_lwd", "edge_lwd_fg", "edge_type", "flow", "mc_col", "mc1", "mc2", "time1", "time2", "type1", "type2", "x1", "x2", "y1", "y2",
# plot_sample_scatter:
"cell_type", "color", "color_values", "egc_epsilon", "expr_breaks", "frac", "metacell", "samp_id", "Sample",
# plot_sample_scatter : get_var_md:
"samp_id",
# plot_sample_stacked_types:
"# of cells", "Cell type", "cell_type", "color", "Fraction", "metacell", "samp_id", "Sample",
# plot_type_predictions_bar:
"cell_type", "color", "fraction", "metacell", "type",
# plot_vein:
".",
# projection_selectors:
"default_gene1",
# qc_ecdf:
"x", "y",
# read_metacell_graphs : <anonymous>:
"from", "to", "weight",
# render_2d_plotly:
"cell_type", "metacell", "query", "weight",
# render_2d_plotly : plot_2d_atlas_proj:
"cell_type", "metacell", "query", "weight", "Weight",
# render_mc_mc_gene_diff_table:
"gene", "Gene", "pval", "type",
# render_mc_mc_gene_plotly:
"cell_type", "fitted_gene",
# scatter_box_outputs:
"default_gene1", "default_gene2", "egc_epsilon", "metacell",
# select_top_fold_genes_per_metacell:
"fp", "gene", "metacell",
# top_correlated_selector:
"project",
# top_correlated_selector_multiple_genes:
"project",
# update_metacell_types:
"cell_type", "metacell",
# update_metadata:
"metacell",
# verify_gene_modules:
"gene",
# zero_fold_gene_plot:
"avg", "Expected", "Expression", "FC", "gene", "Gene", "metacell", "Metacell", "obs", "Observed", "type", "Type", "zero_fold",
# zero_fold_table:
"avg", "Expected", "Expression", "FC", "gene", "metacell", "obs", "type", "zero_fold",
":=", "sec_ord", "metacell_names", "scdb_mctnetwork", "scdb_mc", "mctnetwork_get_flow_mat",
"mc_data", "ord_mean"
)))
tanaylab/MCView documentation built on June 1, 2025, 8:08 p.m.
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globalVariables(unique(c(
# add_gene_modules:
"gene", "module",
# add_genes_to_gene_module:
"gene",
# add_markers_colorbars:
"metacell",
# app_server:
"cell_type", "color", "config", "module", "project", "tab_defs",
# app_server : dataset:
"project",
# app_ui:
"project", "tab_defs",
# atlas_gene_gene:
"default_gene1", "default_gene2", "egc_epsilon",
# calc_ct_ct_gene_df:
"egc_epsilon",
# calc_gene_modules:
"clust", "gene", "module",
# calc_gg_mc_top_cor:
"col1", "col2", "val",
# calc_mc_mc_gene_df:
"egc_epsilon",
# calc_obs_exp_mc_df:
"egc_epsilon",
# calc_obs_exp_type_df:
"egc_epsilon",
# calc_samp_mc_count:
"mc_data", "metacell", "samp_id",
# calc_samp_mc_frac:
"mc_data",
# calc_samp_metadata:
"mc_data", "samp_id",
# calc_samp_samp_gene_df:
"egc_epsilon",
# calc_samples_list:
"mc_data",
# cell_metadata_to_metacell:
"cat_var_n", "cat_varp", "cell_id", "metacell",
# cell_metadata_to_metacell_from_h5ad:
"cell_id", "metacell_name", "outlier",
# cell_type_gene_boxplot:
"Cell type", "cell_type", "egc_epsilon", "expr_breaks", "metacell",
# cell_type_metadata_boxplot:
"Cell type", "cell_type", "metacell",
# cell_type_metadata_confusion:
"# of metacells", "% of cell type metacells", "Cell type", "cell_type", "color", "metacell", "n_tot", "n_tot_md", "p_cell_type", "p_md", "total # of cell type metacells",
# choose_markers:
"fp", "gene", "metacell",
# clipboard_reactives:
"cell_type", "metacell",
# clipboard_reactives : <anonymous>:
"cell_type", "metacell",
# colored_metacell_selector:
"config",
# compute_umap:
"idx", "k", "mc1", "mc2", "weight",
# config_shiny_cache:
"config", "project",
# download_modal_reactives : <anonymous>:
"project",
# dt_selector_column:
"cell_type",
# filter_mat_by_cell_types:
"cell_type", "metacell",
# fitted_genes_per_cell_type_plot:
"cell_type", "color", "type",
# fitted_genes_per_cell_type_table:
"common", "fitted_gene_of", "gene", "type",
# gene_correction_factor_scatter_plot:
"Correction factor", "correction_factor", "gene", "Gene", "Max expression", "max_expr", "type", "Type",
# gene_correction_factor_table:
"correction_factor", "gene", "Max expression", "max_expr", "type",
# gene_inner_fold_scatter_plot:
"# of metacells", "gene", "Gene", "Max expression", "max_expr", "significant_inner_folds_count", "type", "Type",
# gene_inner_fold_table:
"# of metacells", "gene", "Max expression", "max_expr", "significant_inner_folds_count", "type",
# gene_label:
"gene", "module",
# get_cell_type_colors:
"cell_type", "color",
# get_cell_type_data:
"cell_type", "mc_data",
# get_cell_types_mat:
"cell_type", "metacell",
# get_marker_genes:
"config",
# get_markers:
"cache_dir",
# get_mc_color_key:
"cell_type", "mc_col",
# get_mc_config:
"config",
# get_mc_data:
"mc_data",
# get_mc_gene_modules_egc:
"module",
# get_metacell_types_data:
"cell_type", "color", "mc_data", "metacell",
# get_metadata:
"mc_data",
# get_module_genes:
"gene",
# get_samples_egc:
"cell_type", "metacell",
# get_samples_mat:
"cell_type", "metacell",
# get_top_cor_gene:
"egc_epsilon", "gene1", "gene2", "label",
# golem_add_external_resources:
"config",
# group_selectors:
"cell_type", "metacell",
# group_selectors_mod_query:
"cell_type", "metacell",
# has_atlas:
"mc_data",
# heatmap_matrix_reactives:
"cell_type", "config", "metacell",
# heatmap_reactives : <anonymous>:
"cell_type", "color", "type",
# heatmap_sidebar:
"config",
# help_reactives:
"config", "help_config",
# import_atlas:
"atlas", "cell_type", "color", "dtype", "gene", "metacell", "projected_type", "similar", "top1_gene", "top1_lfp", "top2_gene", "top2_lfp", "type", "value", "weight",
# import_cell_metadata:
"cell_id", "metacell", "samp_id",
# import_dataset:
"cell_type", "cluster", "color", "correction_factor", "fp", "gene", "gene1", "gene2", "grouped", "metacell", "significant_inner_folds_count", "total_umis",
# import_dataset_metacell1:
"cell_type", "color", "metacell", "time_bin",
# init_config:
"config",
# init_selected_genes:
"config", "project",
# init_tab_defs:
"config", "tab_defs",
# init_temp_scdb:
".",
# initial_proj_point_size:
"config",
# initial_proj_stroke:
"config",
# initial_scatters_point_size:
"config",
# initial_scatters_stroke:
"config",
# layout_and_graph_to_mc2d:
"from", "metacell", "to",
# load_all_data:
"project",
# load_all_mc_data:
".", "mc_data",
# load_all_mc_data_atlas:
".", "mc_data",
# load_default_2d_projection:
"i", "j", "x", "y",
# load_outliers:
"fp",
# mc2d_plot_gene_ggp:
"cell_type", "egc_epsilon", "enrich", "expr_clipped", "mc_age", "metacell",
# mc2d_plot_metadata_ggp:
"Cell type", "cell_type", "mc_age", "mc_col", "metacell", "top1_gene", "top1_lfp", "top2_gene", "top2_lfp",
# mc2d_to_graph_df:
"d", "dx", "dy", "from", "mc1", "mc2", "metacell", "range_x", "range_y", "to", "weight", "x", "x_mc1", "x_mc2", "y", "y_mc1", "y_mc2",
# mc_mc_gene_scatter_df_reactive:
"cell_type", "metacell",
# mctnetwork_g_t_types:
"flow", "g_src", "g_targ", "mc_t1", "mc_t2", "src_g", "targ_g", "time1", "time2", "type1", "type2",
# metacell_colors_reactive:
"mc_col", "metacell",
# metacell_from_coords_proj:
"diff1", "diff2",
# metacell_selector:
"config",
# metacell_selectors:
"config",
# metacell_selectors_mod_query:
"cell_type", "config",
# metacells_to_types:
"cell_type", "metacell",
# min_edge_length:
"config",
# mod_about_server : <anonymous>:
"cell_type", "color", "default_gene1", "default_gene2", "x", "x_mc1", "x_mc2", "y", "y_mc1", "y_mc2",
# mod_about_ui:
"about_file", "config",
# mod_annotate_server : <anonymous>:
"color", "metacell", "project",
# mod_annotate_server : <anonymous> : <anonymous>:
"color", "metacell", "top1_gene", "top1_lfp", "top2_gene", "top2_lfp",
# mod_atlas_server : <anonymous>:
"project",
# mod_cell_type_server : <anonymous>:
"default_gene1", "egc_epsilon",
# mod_flow_server : <anonymous>:
"cell_type", "color", "default_gene1", "metacell",
# mod_gene_module_controllers:
"gene", "module",
# mod_gene_module_controllers : <anonymous>:
"gene", "module",
# mod_manifold_server : <anonymous>:
"mc1", "mc2", "project",
# mod_manifold_server : <anonymous> : <anonymous>:
"mc1", "mc2",
# mod_outliers_server : <anonymous>:
"cell_id", "metacell", "most_similar",
# mod_projection_qc_server : <anonymous>:
"fitted_gene_any", "gene", "marker_gene",
# mod_query_server : <anonymous>:
"cell_type", "default_gene1", "fitted_gene", "fitted_gene_any", "marker_gene", "metacell",
# mod_samples_server : <anonymous>:
"default_gene1", "default_gene2", "samp_id",
# modify_gene_names:
"alt_name", "gene_name", "new_name",
# observe_mc_click_event:
"cell_type", "metacell",
# observer_mc_select_event:
"cell_type", "metacell",
# order_mc_by_most_var_genes:
".", "cell_type", "ct_ord", "glob_ord", "metacell", "orig_ord", "rand",
# parse_cell_type_colors:
"cell_type", "cluster", "color",
# parse_metacell_types:
"age", "cluster", "metacell",
# parse_metadata:
"metacell",
# plot_gene_time_over_mc:
"Age", "Cell type", "cell_type", "egc_epsilon", "expr_breaks", "mc_age", "metacell", "Metacell",
# plot_gene_trajectory:
"egc_epsilon", "expr_breaks", "gene", "Gene", "time_bin", "time_desc",
# plot_gg_over_mc:
"Cell type", "cell_type", "egc_epsilon", "expr_breaks", "mc_age", "metacell", "Metacell",
# plot_markers_mat:
"cell_type", "color",
# plot_mc_mc_gene:
"expr_breaks", "gene", "Gene", "pval",
# plot_mc_scatter:
"cell_type", "color", "color_values", "egc_epsilon", "expr_breaks", "metacell", "Metacell",
# plot_mc_time_dist:
"Metacell age (E[t])", "n_cells", "time_bin", "time_desc",
# plot_obs_proj_scatter:
"cell_type", "color", "color_values", "egc_epsilon", "expr_breaks", "metacell", "Metacell", "query", "weight",
# plot_propagation_net_metacell:
"cell_type", "cell_type1", "edge_lwd", "edge_lwd_fg", "edge_type", "flow", "mc_col", "mc1", "mc2", "time1", "time2", "type1", "type2", "x1", "x2", "y1", "y2",
# plot_sample_scatter:
"cell_type", "color", "color_values", "egc_epsilon", "expr_breaks", "frac", "metacell", "samp_id", "Sample",
# plot_sample_scatter : get_var_md:
"samp_id",
# plot_sample_stacked_types:
"# of cells", "Cell type", "cell_type", "color", "Fraction", "metacell", "samp_id", "Sample",
# plot_type_predictions_bar:
"cell_type", "color", "fraction", "metacell", "type",
# plot_vein:
".",
# projection_selectors:
"default_gene1",
# qc_ecdf:
"x", "y",
# read_metacell_graphs : <anonymous>:
"from", "to", "weight",
# render_2d_plotly:
"cell_type", "metacell", "query", "weight",
# render_2d_plotly : plot_2d_atlas_proj:
"cell_type", "metacell", "query", "weight", "Weight",
# render_mc_mc_gene_diff_table:
"gene", "Gene", "pval", "type",
# render_mc_mc_gene_plotly:
"cell_type", "fitted_gene",
# scatter_box_outputs:
"default_gene1", "default_gene2", "egc_epsilon", "metacell",
# select_top_fold_genes_per_metacell:
"fp", "gene", "metacell",
# top_correlated_selector:
"project",
# top_correlated_selector_multiple_genes:
"project",
# update_metacell_types:
"cell_type", "metacell",
# update_metadata:
"metacell",
# verify_gene_modules:
"gene",
# zero_fold_gene_plot:
"avg", "Expected", "Expression", "FC", "gene", "Gene", "metacell", "Metacell", "obs", "Observed", "type", "Type", "zero_fold",
# zero_fold_table:
"avg", "Expected", "Expression", "FC", "gene", "metacell", "obs", "type", "zero_fold",
":=", "sec_ord", "metacell_names", "scdb_mctnetwork", "scdb_mc", "mctnetwork_get_flow_mat",
"mc_data", "ord_mean"
)))
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