microbiome/miaViz
Microbiome Analysis Plotting and Visualization

Package index
Search the microbiome/miaViz package
Vignettes
Functions
183
Source code
30
Man pages
17
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microbiome/miaViz: Microbiome Analysis Plotting and Visualization
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API

API for microbiome/miaViz
Microbiome Analysis Plotting and Visualization

Global functions
.abund_plotter Source code
.abund_plotter_incorporate_metadata 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_paired_samples 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
.calculate_max_and_min_for_loadings Source code
.check_abundance_input 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_rda_baseplot 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_eigenvalues Source code
.get_feature_info 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_rda_attribute Source code
.get_rda_centroids_data Source code
.get_rda_ellipse_data Source code
.get_rda_species_data Source code
.get_rda_vector_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_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_other_fields Source code
.order_abundance_cols Source code
.order_abundance_rows Source code
.order_tree Source code
.plot_bar_or_lollipop 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
.prepare_data Source code
.prevalence_plotter Source code
.process_component Source code
.radial_theta Source code
.rda2tse Source code
.rda_plotter Source code
.rda_plotter_centroids_or_species Source code
.rda_plotter_ellipse Source code
.rda_plotter_vector Source code
.remove_taxonomic_level_from_labels Source code
.resolve_plot_colours Source code
.scree_plotter Source code
.series_plotter Source code
.subset_constrained_rda 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
plotScree Man page
plotScree,ANY-method Man page
plotScree,SingleCellExperiment-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
microbiome/miaViz documentation built on Dec. 9, 2024, 2:18 a.m.

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