Package index • cellucid

Write a Cellucid-ready AnnData

cellucid_prepare(): Write single-cell data as a Cellucid-ready AnnData (or MuData) store
cellucid_restore_original_order(): Put the cells of a Cellucid-ready file back in the order they were given
cellucid_transition_drift(): Compute transition drift in embedding space

Subsample the cells

cellucid_subsample_cells(): The cells a Cellucid subsample keeps

View from R

cellucid_view() cellucid_serve() cellucid_stop() cellucid_stop_all() cellucid_viewers(): View an R object or a file in the Cellucid viewer
cellucid_act() cellucid_action_result() cellucid_freeze(): Do anything in an open Cellucid viewer: send an action, collect its answer
cellucid_on() cellucid_off() cellucid_selection() cellucid_wait_ready() cellucid_request_session() cellucid_session_result(): React to what happens in an open Cellucid viewer
cellucid_mcp(): Let an agent app on this computer work in a Cellucid viewer
cellucid_debug_connection(): Check what works between R and an open Cellucid viewer
cellucid_clear_web_cache(): Remove the cached Cellucid web app

The viewer’s actions

cellucid_analysis_cancel(): Stop an analysis
cellucid_analysis_close(): Close the open analysis
cellucid_analysis_composition_get(): Read composition options
cellucid_analysis_composition_set(): Set composition options
cellucid_analysis_correlation_get(): Read correlation options
cellucid_analysis_correlation_set(): Set correlation options
cellucid_analysis_detailed_set(): Choose what the detailed analysis plots
cellucid_analysis_differential_get(): Read differential expression options
cellucid_analysis_differential_set(): Set differential expression options
cellucid_analysis_dotplot_get(): Read dot plot options
cellucid_analysis_dotplot_set(): Set dot plot options
cellucid_analysis_list(): List the analyses
cellucid_analysis_markers_get(): Read marker genes options
cellucid_analysis_markers_set(): Set marker genes options
cellucid_analysis_open(): Open an analysis
cellucid_analysis_pages_set(): Choose the pages of an analysis
cellucid_analysis_quick_set(): Choose the fields of the quick analysis
cellucid_analysis_result(): Read an analysis result
cellucid_analysis_run(): Run an analysis
cellucid_analysis_signature_get(): Read gene signature options
cellucid_analysis_signature_set(): Set gene signature options
cellucid_analysis_size_set(): Size an analysis's expanded view
cellucid_analysis_view_set(): Change how an analysis is shown
cellucid_analysis_window_close(): Close an analysis window
cellucid_analysis_window_collapse(): Collapse or expand an analysis window
cellucid_analysis_window_copy(): Copy an analysis window
cellucid_analysis_window_place(): Move or resize an analysis window
cellucid_annotation_suggest(): Suggest a label
cellucid_annotation_suggestions(): Read the community annotation
cellucid_annotation_vote(): Vote on a suggested label
cellucid_camera_navigation_set(): Set the navigation mode
cellucid_camera_path_clear(): Clear the camera path
cellucid_camera_path_duration_set(): Set a camera path transition time
cellucid_camera_path_keyframe_add(): Add a camera path keyframe
cellucid_camera_path_keyframe_move(): Move a camera path keyframe
cellucid_camera_path_keyframe_remove(): Delete a camera path keyframe
cellucid_camera_path_keyframe_rename(): Rename a camera path keyframe
cellucid_camera_path_loop_back_set(): End the camera path at its start
cellucid_camera_path_playback_set(): Set camera path playback
cellucid_camera_reset(): Reset the camera
cellucid_camera_set(): Place the camera
cellucid_category_delete(): Delete a category
cellucid_category_merge(): Merge two categories
cellucid_category_rename(): Rename a category
cellucid_cells_export(): Export the highlighted cells
cellucid_cells_open(): Open a share of the cells
cellucid_cells_read_genes(): Read genes for more cells
cellucid_cells_values(): Read values of cells
cellucid_cells_visibility_set(): Hide or show cells
cellucid_color_by(): Colour the cells by a field or gene
cellucid_color_category(): Colour one category
cellucid_color_continuous_colormap(): Choose a colour map
cellucid_color_continuous_log(): Log colour scale
cellucid_color_continuous_range(): Set the colour range
cellucid_color_continuous_rescale(): Rescale colours to the visible range
cellucid_color_continuous_zero_gray(): Gray for zero
cellucid_dataset_open(): Open a dataset
cellucid_dataset_share_link(): Make a share link
cellucid_dataset_summary(): Read the dataset summary
cellucid_datasets_list(): List the datasets to open
cellucid_display_reset(): Reset the camera and display
cellucid_field_categories(): Read the categories of a field
cellucid_field_consensus(): Build the consensus column
cellucid_field_create_from_pages(): Make a field from highlight pages
cellucid_field_delete(): Delete a field
cellucid_field_duplicate(): Duplicate a field
cellucid_field_export(): Export a field
cellucid_field_purge(): Purge a deleted field
cellucid_field_push(): Add a column of values
cellucid_field_rename(): Rename a field
cellucid_field_restore(): Restore a deleted field
cellucid_field_revert_name(): Restore a field's original name
cellucid_field_summary(): Summarise a field per category
cellucid_fields_list(): List the fields
cellucid_figure_export(): Export the figure
cellucid_figure_export_set(): Change figure export settings
cellucid_filter_category_all(): Show or hide every category
cellucid_filter_category_cell_count(): Keep N cells of a category
cellucid_filter_category_missing(): Show or hide cells without a category
cellucid_filter_category_visibility(): Show or hide categories
cellucid_filter_continuous_range(): Set a visible range
cellucid_filter_continuous_reset(): Reset a visible range
cellucid_filter_enable(): Turn a filter on or off
cellucid_filter_outlier(): Filter outliers
cellucid_filter_remove(): Remove a filter
cellucid_gene_set_save(): Keep a gene set
cellucid_genes_search(): Search the genes
cellucid_highlight_category(): Highlight a category
cellucid_highlight_cells(): Highlight cells
cellucid_highlight_clear_all(): Clear every highlight
cellucid_highlight_group_remove(): Remove a highlight group
cellucid_highlight_group_toggle(): Show or hide a highlight group
cellucid_highlight_page_clear(): Clear a highlight page
cellucid_highlight_page_combine(): Combine two highlight pages
cellucid_highlight_page_create(): Make a highlight page
cellucid_highlight_page_delete(): Delete a highlight page
cellucid_highlight_page_recolor(): Recolour a highlight page
cellucid_highlight_page_rename(): Rename a highlight page
cellucid_highlight_page_switch(): Show a highlight page
cellucid_highlight_range(): Highlight a range of values
cellucid_history_anndata_save(): Save AnnData with this state
cellucid_history_bookmark_set(): Bookmark a step
cellucid_history_branch_apply(): Apply a branch's steps here
cellucid_history_branch_archive(): Archive a branch
cellucid_history_branch_cancel(): Cancel a new branch
cellucid_history_branch_create(): Branch here
cellucid_history_branch_delete(): Delete a branch
cellucid_history_branch_lock(): Lock a branch
cellucid_history_branch_rename(): Rename a branch
cellucid_history_branch_set_main(): Make a branch main
cellucid_history_branch_switch(): Switch branch
cellucid_history_branch_without(): Branch without a step
cellucid_history_clear(): Clear the history
cellucid_history_diff(): Compare two steps
cellucid_history_get(): Read the history
cellucid_history_group_create(): Group steps
cellucid_history_group_extend(): Add steps to a group
cellucid_history_group_remove(): Ungroup
cellucid_history_group_rename(): Rename a group
cellucid_history_journal_empty(): Empty Recently deleted
cellucid_history_journal_undo(): Restore from Recently deleted
cellucid_history_jump(): Show a step
cellucid_history_methods(): Write the methods paragraph
cellucid_history_note_add(): Add a note
cellucid_history_note_edit(): Edit a note
cellucid_history_note_remove(): Remove a note
cellucid_history_pseudocode(): Write the pseudocode
cellucid_history_recording_pause(): Pause recording
cellucid_history_recording_resume(): Resume recording
cellucid_history_redo(): Redo
cellucid_history_replay(): Replay a saved history
cellucid_history_report(): Make the printable report
cellucid_history_save(): Save the history in this browser
cellucid_history_saved_delete(): Delete a saved state
cellucid_history_saved_list(): List saved states
cellucid_history_search(): Search the history
cellucid_history_share(): Share the history as a file
cellucid_history_squash(): Merge steps into one
cellucid_history_stale(): List stale results
cellucid_history_step(): Read a step
cellucid_history_step_delete(): Delete a step
cellucid_history_step_revert(): Revert a step
cellucid_history_summary(): Summarise the history
cellucid_history_tour_start(): Start the guided tour
cellucid_history_tour_stop(): Stop the guided tour
cellucid_history_tracker_remove(): Remove a tracker
cellucid_history_tracker_rename(): Rename a tracker
cellucid_history_tracker_start(): Start another tracker
cellucid_history_tracker_use(): Use another tracker
cellucid_history_turn_undo(): Undo a turn
cellucid_history_undo(): Undo
cellucid_history_verify(): Verify a branch
cellucid_layout_get(): Read the layout
cellucid_layout_panel_dock(): Dock a section
cellucid_layout_panel_float(): Undock a section
cellucid_layout_panel_place(): Move or resize a floating section
cellucid_layout_section_open(): Open or close a section
cellucid_layout_sidebar_show(): Show or hide the sidebar
cellucid_layout_sidebar_width(): Resize the sidebar
cellucid_layout_theme_set(): Choose the theme
cellucid_mapping_set(): Change the data mapping
cellucid_my_datasets_forget(): Forget a dataset of My datasets
cellucid_setting_set(): Change a setting
cellucid_settings_list(): List the settings
cellucid_stored_list(): List what this browser keeps
cellucid_stored_remove(): Remove what this browser keeps
cellucid_view_cameras_link(): Link cameras
cellucid_view_clear(): Remove every kept view
cellucid_view_embedding_cycle(): Next embedding of a dimension
cellucid_view_embedding_default(): Show the default embedding
cellucid_view_embedding_set(): Show an embedding
cellucid_view_focus(): Select a view
cellucid_view_keep(): Keep the view
cellucid_view_layout_set(): Set the view layout
cellucid_view_picture(): Take a picture of a view
cellucid_view_remove(): Remove a view
cellucid_views_state(): Read the views

Results back into R

cellucid_pull() cellucid_results() cellucid_subset() cellucid_gene_sets(): Bring what was made in Cellucid back onto the object, in one call
cellucid_push() cellucid_write_gmt() cellucid_read_gmt(): Show a column in Cellucid, and read or write GMT files

Sessions and the history

cellucid_read_session() cellucid_conversations(): Read a saved Cellucid session: its history, checked whole
cellucid_trackers() cellucid_tracker() cellucid_branches() cellucid_branch() cellucid_groups() cellucid_group() cellucid_steps() cellucid_step() cellucid_step_state() cellucid_step_diff() cellucid_stale() cellucid_notes() cellucid_turns() cellucid_journal() cellucid_methods() cellucid_pseudocode(): Read a Cellucid history: trackers, branches, groups, steps, notes, turns
cellucid_apply_session() cellucid_apply_plan() cellucid_history_applied(): Apply one step of a saved Cellucid history to an object: a plan first
cellucid_turn() cellucid_last_history_change(): The viewer's history, live: notebook turns and what changed
cellucid_load_session() cellucid_load_session_result(): Push a saved Cellucid session into the viewer