plot.de.lorean

Type of plot:<ul>
<li>'expr.data': The expression data plotted by capture time.
 See <code><a rd-options="" href="/link/expr.data.plot?package=DeLorean&version=1.5.0" data-mini-rdoc="DeLorean::expr.data.plot">expr.data.plot</a></code>.</li>
<li>'Rhat': \(hat{R}\) convergence statistics
 See <code><a rd-options="" href="/link/Rhat.plot?package=DeLorean&version=1.5.0" data-mini-rdoc="DeLorean::Rhat.plot">Rhat.plot</a></code>.</li>
<li>'pseudotime': Pseudotimes in best posterior sample
 See <code><a rd-options="" href="/link/pseudotime.plot?package=DeLorean&version=1.5.0" data-mini-rdoc="DeLorean::pseudotime.plot">pseudotime.plot</a></code>.</li>
<li>'profiles': Gene expression profiles for best posterior sample
 See <code><a rd-options="" href="/link/profiles.plot?package=DeLorean&version=1.5.0" data-mini-rdoc="DeLorean::profiles.plot">profiles.plot</a></code>.</li>
<li>'tau.offsets': Offsets of pseudotimes to assess the prior
 See <code><a rd-options="" href="/link/tau.offsets.plot?package=DeLorean&version=1.5.0" data-mini-rdoc="DeLorean::tau.offsets.plot">tau.offsets.plot</a></code>.</li>
<li>'marg.like': Plot the posterior of the marginal likelihoods
 for individual genes.
 See <code><a rd-options="" href="/link/marg.like.plot?package=DeLorean&version=1.5.0" data-mini-rdoc="DeLorean::marg.like.plot">marg.like.plot</a></code>.</li>
<li>'roughnesses': Roughnesses of the pseudotime posterior
 See <code><a rd-options="" href="/link/roughnesses.plot?package=DeLorean&version=1.5.0" data-mini-rdoc="DeLorean::roughnesses.plot">roughnesses.plot</a></code>.</li>
<li>'init.vs.pseudotimes': Plot the initialisations used against the pseudotimes estimated
 See <code><a rd-options="" href="/link/init.orderings.vs.pseudotimes.plot?package=DeLorean&version=1.5.0" data-mini-rdoc="DeLorean::init.orderings.vs.pseudotimes.plot">init.orderings.vs.pseudotimes.plot</a></code>.</li>
</ul>

type

Implements the DeLorean model (Reid & Wernisch (2016)
<doi:10.1093/bioinformatics/btw372>) to estimate pseudotimes for
single cell expression data. The DeLorean model uses a Gaussian process
latent variable model to model uncertainty in the capture time of
cross-sectional data.

John Reid

DeLorean

Estimates Pseudotimes for Single Cell Expression Data

plot.de.lorean function

Type of plot:<ul>
<li>'expr.data': The expression data plotted by capture time.
 See <code><a rd-options='' href='expr.data.plot'>expr.data.plot</a></code>.</li>
<li>'Rhat': \(hat{R}\) convergence statistics
 See <code><a rd-options='' href='Rhat.plot'>Rhat.plot</a></code>.</li>
<li>'pseudotime': Pseudotimes in best posterior sample
 See <code><a rd-options='' href='pseudotime.plot'>pseudotime.plot</a></code>.</li>
<li>'profiles': Gene expression profiles for best posterior sample
 See <code><a rd-options='' href='profiles.plot'>profiles.plot</a></code>.</li>
<li>'tau.offsets': Offsets of pseudotimes to assess the prior
 See <code><a rd-options='' href='tau.offsets.plot'>tau.offsets.plot</a></code>.</li>
<li>'marg.like': Plot the posterior of the marginal likelihoods
 for individual genes.
 See <code><a rd-options='' href='marg.like.plot'>marg.like.plot</a></code>.</li>
<li>'roughnesses': Roughnesses of the pseudotime posterior
 See <code><a rd-options='' href='roughnesses.plot'>roughnesses.plot</a></code>.</li>
<li>'init.vs.pseudotimes': Plot the initialisations used against the pseudotimes estimated
 See <code><a rd-options='' href='init.orderings.vs.pseudotimes.plot'>init.orderings.vs.pseudotimes.plot</a></code>.</li>
</ul>

plot.de.lorean: Various DeLorean object plots

Description

Usage

Arguments