def_wrapper

create_ti_method

Provides functionality to infer trajectories from single-cell data,
represent them into a common format, and adapt them. Other biological information
can also be added, such as cellular grouping, RNA velocity and annotation.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.

Robrecht Cannoodt

dynwrap

Representing and Inferring Single-Cell Trajectories

Wouter Saelens

def_wrapper function

<dl><dt>input_required</dt>
<dd>The required inputs for this method. See <code>dynwrap::allowed_inputs()</code>.</dd>
<dt>input_optional</dt>
<dd>Optional inputs for this method. See <code>dynwrap::allowed_inputs()</code>.</dd>
<dt>type</dt>
<dd>Which type of trajectory post-processing is used. Possible values:
<code>"trajectory"</code> (default), <code>"linear_trajectory"</code>, <code>"cyclic_trajectory"</code>, <code>"branch_trajectory"</code>,
<code>"cluster_graph"</code>, <code>"dimred_projection"</code>, <code>"end_state_probabilities"</code>, <code>"cell_graph"</code>.</dd>
<dt>topology_inference</dt>
<dd>Whether the topology is fixed (<code>"fixed"</code>), free (<code>"free"</code>),
or fixed by a parameter provided to the algorithm (<code>"param"</code>).</dd>
<dt>trajectory_types</dt>
<dd>The possible trajectory types this method can return. Must be a subset of
<code>c("cyclic", "linear", "bifurcation", "convergence", "multifurcation", "tree", "graph", "acyclic_graph", "disconnected_graph")</code></dd></dl>

Arguments

Meta information on the wrapper — def_wrapper

<dl>

<dt>input_required</dt>
<dd>The required inputs for this method. See <code>dynwrap::allowed_inputs()</code>.</dd>


<dt>input_optional</dt>
<dd>Optional inputs for this method. See <code>dynwrap::allowed_inputs()</code>.</dd>


<dt>type</dt>
<dd>Which type of trajectory post-processing is used. Possible values:
<code>"trajectory"</code> (default), <code>"linear_trajectory"</code>, <code>"cyclic_trajectory"</code>, <code>"branch_trajectory"</code>,
<code>"cluster_graph"</code>, <code>"dimred_projection"</code>, <code>"end_state_probabilities"</code>, <code>"cell_graph"</code>.</dd>


<dt>topology_inference</dt>
<dd>Whether the topology is fixed (<code>"fixed"</code>), free (<code>"free"</code>),
or fixed by a parameter provided to the algorithm (<code>"param"</code>).</dd>


<dt>trajectory_types</dt>
<dd>The possible trajectory types this method can return. Must be a subset of
<code>c("cyclic", "linear", "bifurcation", "convergence", "multifurcation", "tree", "graph", "acyclic_graph", "disconnected_graph")</code></dd>

</dl>

def_wrapper: Meta information on the wrapper

Description

Usage

Arguments

Examples