Index A | B | C | D | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V A active_dataset (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) add_annotations() (in module goatpy.he_image) Add_Pseudo_Image() (in module goatpy.pseudo_image) add_qupath_annotations() (in module goatpy.annotation) add_uns() (in module goatpy.pseudo_image) align_image_using_landmarks() (in module goatpy.landmark_alignment) AnalysisSidebar (class in goatpy.analysis_gui) annotate_glycans() (in module goatpy.tools) annotated_highlight_mzs (goatpy.analysis_gui.SpectrumWidget attribute) annotated_highlight_tol (goatpy.analysis_gui.SpectrumWidget attribute) annotations_to_pixels() (in module goatpy.annotation) applied_tolerance (goatpy.analysis_gui.SpectrumWidget attribute) B BASE_STYLE (in module goatpy.analysis_gui) batch_correction() (in module goatpy.batch_correction) bin_and_align() (in module goatpy.bin) bin_imzml() (in module goatpy.bin) C CATEGORICAL_CMAPS (in module goatpy.analysis_gui) centroids_to_pixel_squares() (in module goatpy.io) check_batch() (in module goatpy.plotting) clear_all() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) clear_annotated_highlights() (goatpy.analysis_gui.SpectrumWidget method) clear_highlight() (goatpy.analysis_gui.SpectrumWidget method) CONTINUOUS_CMAPS (in module goatpy.analysis_gui) create_image_from_data() (in module goatpy.pseudo_image) D display_unregistered_ion_image() (goatpy.analysis_gui.AnalysisSidebar method) F fig (goatpy.analysis_gui.MplCanvas attribute) figure (goatpy.analysis_gui.MplCanvas attribute) filter_spatialdata() (in module goatpy.filter) G generate_continuous_bins() (in module goatpy.pseudo_image) generate_random_colors() (in module goatpy.pseudo_image) get_kmean_clusters() (in module goatpy.graphpca_mod) getimage() (in module goatpy.io) glycan_df (goatpy.analysis_gui.AnalysisSidebar attribute) (goatpy.analysis_gui.SpectrumWidget attribute) GLYCAN_LAYER_NAME (in module goatpy.analysis_gui) glycan_list (goatpy.analysis_gui.GlycanSelectionDialog attribute) glycan_names (goatpy.analysis_gui.GlycanSelectionDialog attribute) glycan_reference_df (goatpy.analysis_gui.AnalysisSidebar attribute) glycan_selected (goatpy.analysis_gui.AnalysisSidebar attribute) GlycanSelectionDialog (class in goatpy.analysis_gui) glyco_spatialdata() (in module goatpy.io) goatpy module goatpy.analysis_gui module goatpy.annotation module goatpy.auto_align module goatpy.batch_correction module goatpy.bin module goatpy.data module goatpy.filter module goatpy.graphpca_mod module goatpy.he_image module goatpy.io module goatpy.landmark_alignment module goatpy.plotting module goatpy.preprocessing module goatpy.pseudo_image module goatpy.tools module GOATPY_VIZ_KEY (in module goatpy.analysis_gui) graphpca_spatialdata() (in module goatpy.graphpca_mod) H he_image_key (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) he_landmarks (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) he_scale_factor (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) he_scale_level (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) he_sd (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) he_spatialdata() (in module goatpy.he_image) highlight_glycan() (goatpy.analysis_gui.SpectrumWidget method) highlighted_label (goatpy.analysis_gui.SpectrumWidget attribute) highlighted_mz (goatpy.analysis_gui.SpectrumWidget attribute) hmap_custom_indices (goatpy.analysis_gui.AnalysisSidebar attribute) I ihc_spatialdata() (in module goatpy.io) init_ui() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) K keyPressEvent() (goatpy.analysis_gui.GlycanSelectionDialog method) kneighbors_graph_spatial() (in module goatpy.graphpca_mod) L label_to_mz (goatpy.analysis_gui.GlycanSelectionDialog attribute) LandmarkAlignmentWidget (class in goatpy.landmark_alignment) launch_goatpy_gui() (in module goatpy.analysis_gui) launch_landmark_gui() (in module goatpy.landmark_alignment) load_and_align() (in module goatpy.auto_align) M maldi_image_key (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) maldi_landmarks (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) maldi_scale_factor (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) maldi_scale_level (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) maldi_sd (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) map_categories_to_colors() (in module goatpy.pseudo_image) merge_spatialdata() (in module goatpy.tools) module goatpy goatpy.analysis_gui goatpy.annotation goatpy.auto_align goatpy.batch_correction goatpy.bin goatpy.data goatpy.filter goatpy.graphpca_mod goatpy.he_image goatpy.io goatpy.landmark_alignment goatpy.plotting goatpy.preprocessing goatpy.pseudo_image goatpy.tools MplCanvas (class in goatpy.analysis_gui) N nomenclature_updated (goatpy.analysis_gui.AnalysisSidebar attribute) normalize_matrix() (in module goatpy.preprocessing) normalize_spatialdata() (in module goatpy.preprocessing) O on_click_combined() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) on_click_split() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) P PALETTE (in module goatpy.analysis_gui) parmap() (in module goatpy.io) peak_clicked (goatpy.analysis_gui.SpectrumWidget attribute) peak_list (goatpy.analysis_gui.SpectrumWidget attribute) peaks (goatpy.analysis_gui.AnalysisSidebar attribute) (goatpy.analysis_gui.GlycanSelectionDialog attribute) (goatpy.analysis_gui.SpectrumWidget attribute) plot_spectra_comparison() (in module goatpy.plotting) plot_spectrum() (in module goatpy.plotting) postpone_transformation() (in module goatpy.landmark_alignment) R rd_peaks() (in module goatpy.io) rd_peaks_from_package() (in module goatpy.io) S save_landmarks() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) save_to_sdata() (goatpy.analysis_gui.AnalysisSidebar method) sdata (goatpy.analysis_gui.AnalysisSidebar attribute) (goatpy.analysis_gui.SpectrumWidget attribute) select_peak_from_spectrum() (goatpy.analysis_gui.AnalysisSidebar method) selected_indices (goatpy.analysis_gui.GlycanSelectionDialog attribute) set_active_dataset() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) set_annotated_highlights() (goatpy.analysis_gui.SpectrumWidget method) setup_layers() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) show_annotated_on_spectra (goatpy.analysis_gui.AnalysisSidebar attribute) SpectrumWidget (class in goatpy.analysis_gui) split_view (goatpy.landmark_alignment.LandmarkAlignmentWidget attribute) summary_lbl (goatpy.analysis_gui.GlycanSelectionDialog attribute) T table_name (goatpy.analysis_gui.AnalysisSidebar attribute) (goatpy.analysis_gui.SpectrumWidget attribute) tabs (goatpy.analysis_gui.GlycanSelectionDialog attribute) TIPS (goatpy.analysis_gui.TipsDialog attribute) TipsDialog (class in goatpy.analysis_gui) type_edit (goatpy.analysis_gui.GlycanSelectionDialog attribute) U undo_last() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) unregistered_peak_display (goatpy.analysis_gui.SpectrumWidget attribute) update_peak_labels() (goatpy.analysis_gui.SpectrumWidget method) update_status() (goatpy.landmark_alignment.LandmarkAlignmentWidget method) upload_lbl (goatpy.analysis_gui.GlycanSelectionDialog attribute) V viewer (goatpy.analysis_gui.AnalysisSidebar attribute)
