API Reference Coverage#
cellucid-r exports the writer cellucid_prepare(), which writes a
Cellucid-ready AnnData (or MuData) store, cellucid_transition_drift(), which
computes a vector field for it from a cell-cell transition matrix, the viewer
(cellucid_view(), cellucid_serve() and the functions that talk to an open
viewer), the session reader (cellucid_read_session(), the history’s
reading functions such as cellucid_steps(), and cellucid_apply_session())
and cellucid_clear_web_cache(). This
section is the flat reference for them: every exported function and the
complete argument lists on one page, and the error messages on another. The
narrative explanation of each argument lives in
Data Preparation API and Viewing and Loading.
Note
The R help pages (?cellucid_prepare, ?cellucid_transition_drift,
?cellucid_view, ?cellucid_act, ?cellucid_on, ?cellucid_turn,
?cellucid_load_session, ?cellucid_read_session, ?cellucid_trackers,
?cellucid_apply_session, ?cellucid_debug_connection,
?cellucid_clear_web_cache) are hand-written and authoritative – each
action function’s page (?cellucid_color_by, ?cellucid_highlight_cells, …)
is generated from the action catalogue with the function –, and
cellucid-r’s own test suite rebuilds each \usage block into a function and
compares it to the real signature. The two pages here restate them for the
web, with links into the guide.
Recommended reading order
Every exported function; every argument of cellucid_prepare(), grouped by
what it is for, with its default, where it lands in the store, and the page
that explains it; cellucid_transition_drift() and the viewer’s signatures.
How the package reports problems, and every message it raises, grouped by the input it is about.