Global functions | |
---|---|
.abund_plotter | Source code |
.add_abbr_guide | Source code |
.add_extra_guide_graph | Source code |
.add_extra_guide_tree | Source code |
.add_extra_line_guide | Source code |
.add_graph_data_or_warn | Source code |
.add_graph_labels | Source code |
.add_graph_node_labels | Source code |
.add_label_abbreviations | Source code |
.add_legend | Source code |
.add_signif_to_vector_labels | Source code |
.add_tree_highlight_labels | Source code |
.add_tree_highlights | Source code |
.add_tree_node_labels | Source code |
.calc_highlight_extendto | Source code |
.calc_highlight_label_text_offset | Source code |
.check_abund_plot_args | Source code |
.check_args | Source code |
.check_graph_plot_switches | Source code |
.check_loadings_matrix | Source code |
.check_tree_plot_switches | Source code |
.clean_tree_data | Source code |
.colnames_tbl_graph | Source code |
.combine_tree_and_other_fields | Source code |
.combine_tree_data_and_other_fields | Source code |
.create_treedata_for_plotting | Source code |
.density_plotter | Source code |
.feature_plotter | Source code |
.features_plotter | Source code |
.flip_plot | Source code |
.get_abundance_data | Source code |
.get_cladelab_args | Source code |
.get_density_args | Source code |
.get_edge_args | Source code |
.get_feature_data | Source code |
.get_feature_info | Source code |
.get_features_data | Source code |
.get_graph_data | Source code |
.get_graph_edge_args | Source code |
.get_hightlight_args | Source code |
.get_line_args | Source code |
.get_loadings_matrix | Source code |
.get_loadings_plot_data | Source code |
.get_loadings_tree_data | Source code |
.get_new_var_name_value | Source code |
.get_object_and_trimmed_tree | Source code |
.get_point_args | Source code |
.get_prevalence_count | Source code |
.get_prevalence_plot_data | Source code |
.get_prevalence_plot_matrix | Source code |
.get_prevalence_plot_point_data | Source code |
.get_rect_args | Source code |
.get_ribbon_args | Source code |
.get_series_data | Source code |
.get_tile_data | Source code |
.get_tree_data | Source code |
.get_tree_labels_for_ordering | Source code |
.get_xcoord_mid | Source code |
.graph_plotter | Source code |
.incorporate_density_data | Source code |
.incorporate_graph_vis | Source code |
.incorporate_prevalence_vis | Source code |
.incorporate_rda_vis | Source code |
.incorporate_tree_vis | Source code |
.is_continuous | Source code |
.loadings_tree_plotter | Source code |
.merge_tip_node_tree_data | Source code |
.merge_tree_vis_data | Source code |
.na_replace_from_plot_data | Source code |
.norm_id_col_of_other_fields | Source code |
.norm_label | Source code |
.norm_layout_edge_type | Source code |
.norm_order_sample_by | Source code |
.norm_other_fields | Source code |
.order_abund_feature_data | Source code |
.order_tree | Source code |
.plot_loadings | Source code |
.plot_row_column_graph | Source code |
.plot_row_column_tree | Source code |
.plot_tile_data | Source code |
.plot_tree_edges | Source code |
.plot_tree_node_labels | Source code |
.plot_tree_node_points | Source code |
.plot_tree_plot_highlights | Source code |
.prevalence_plotter | Source code |
.process_component | Source code |
.radial_theta | Source code |
.rda2tse | Source code |
.rda_plotter | Source code |
.remove_taxonomic_level_from_labels | Source code |
.resolve_plot_colours | Source code |
.series_plotter | Source code |
.summarise_tile_data | Source code |
.theme_plotGraph | Source code |
.theme_plotTree | Source code |
.tidy_vector_labels | Source code |
.tile_plotter | Source code |
.tree_plotter | Source code |
colTreeData | Man page |
colTreeData,TreeSummarizedExperiment-method | Man page |
colTreeData<- | Man page |
colTreeData<-,TreeSummarizedExperiment-method | Man page |
col_graph | Man page |
combineTreeData | Man page |
combineTreeData,phylo-method | Man page |
combineTreeData,treedata-method | Man page |
getNeatOrder | Man page |
getNeatOrder,matrix-method | Man page |
mia-datasets | Man page |
mia-plot-args | Man page |
miaViz | Man page |
miaViz-package | Man page |
plotAbundance | Man page |
plotAbundance,SummarizedExperiment-method | Man page |
plotAbundanceDensity | Man page |
plotAbundanceDensity,SummarizedExperiment-method | Man page |
plotCCA | Man page |
plotCCA,SingleCellExperiment-method | Man page |
plotCCA,matrix-method | Man page |
plotColGraph | Man page |
plotColGraph,ANY,SummarizedExperiment-method | Man page |
plotColGraph,SummarizedExperiment,missing-method | Man page |
plotColTile | Man page |
plotColTile,SummarizedExperiment-method | Man page |
plotColTree | Man page |
plotColTree,TreeSummarizedExperiment-method | Man page |
plotDMN | Man page |
plotDMNFit | Man page |
plotDMNFit,SummarizedExperiment-method | Man page |
plotFeaturePrevalence | Man page |
plotFeaturePrevalence,ANY-method | Man page |
plotGraph | Man page |
plotLoadings | Man page |
plotLoadings,SingleCellExperiment-method | Man page |
plotLoadings,TreeSummarizedExperiment-method | Man page |
plotLoadings,matrix-method | Man page |
plotNMDS | Man page Source code |
plotPrevalence | Man page |
plotPrevalence,SummarizedExperiment-method | Man page |
plotPrevalentAbundance | Man page |
plotPrevalentAbundance,SummarizedExperiment-method | Man page |
plotRDA | Man page |
plotRDA,SingleCellExperiment-method | Man page |
plotRDA,matrix-method | Man page |
plotRowGraph | Man page |
plotRowGraph,ANY,SummarizedExperiment-method | Man page |
plotRowGraph,SummarizedExperiment,missing-method | Man page |
plotRowPrevalence | Man page |
plotRowPrevalence,SummarizedExperiment-method | Man page |
plotRowTile | Man page |
plotRowTile,SummarizedExperiment-method | Man page |
plotRowTree | Man page |
plotRowTree,TreeSummarizedExperiment-method | Man page |
plotSeries | Man page |
plotSeries,SummarizedExperiment-method | Man page |
plotTaxaPrevalence | Man page |
plotTaxaPrevalence,ANY-method | Man page |
plotTree | Man page |
rowTreeData | Man page |
rowTreeData,TreeSummarizedExperiment-method | Man page |
rowTreeData<- | Man page |
rowTreeData<-,TreeSummarizedExperiment-method | Man page |
row_graph | Man page |
row_graph_order | Man page |
treeData | Man page |
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