# In DeLorean: Estimates Pseudotimes for Single Cell Expression Data

# Attach the DeLorean data frame to access members
attach(dl)


## Posterior

### Pseudotime

The estimated pseudotime from the best sample against the observed capture time.

plot(dl, type="pseudotime")


The full tau posterior for each cell.

(
ggplot(samples.l$tau %>% arrange(capture), aes(x=cell, y=tau, color=capture)) + geom_boxplot() + coord_flip() )  The posterior of the pseudotime offsets relative to the capture times. We also show the prior on the offset. plot(dl, type="tau.offsets")  ### Between time variation The posterior for the between time variation$\log \psi_g$: (ggplot(samples.l$psi, aes(x=log(psi)))
+ geom_density()
+ geom_rug()
+ stat_function(fun=function(x) dnorm(x,
mean=hyper$mu_psi, sd=hyper$sigma_psi),
colour="blue", alpha=.7, linetype="dashed")
)


Temporal variation by gene:

(ggplot(noise.levels,
aes(x=gene, y=log10(psi), fill=gene %in% genes.high.psi),
environment=environment())
+ geom_boxplot()
+ coord_flip())


### Within time variation

The posterior for the within time variation $\log \omega_g$:

(ggplot(samples.l$omega, aes(x=log(omega))) + geom_density() + geom_rug() + stat_function(fun=function(x) dnorm(x, mean=hyper$mu_omega,
sd=hyper$sigma_omega), colour="blue", alpha=.7, linetype="dashed") )  Within time variation by gene: (ggplot(noise.levels, aes(x=gene, y=log10(omega), fill=gene %in% genes.high.psi), environment=environment()) + geom_boxplot() + coord_flip())  ### Variation comparisons The within time variation compared to the temporal variation (on log-log scale): (ggplot(noise.levels, aes(x=log(psi), y=log(omega), color=gene %in% genes.high.psi), environment=environment()) + geom_point() + geom_abline(intercept=0, slope=1, linetype="dashed", alpha=.7))  have.cell.sizes <- 'S' %in% names(samples.l)    ### Other posteriors The posterior for the model log probability: (ggplot(samples.l$lp__, aes(x=lp__))
+ geom_density()
+ geom_rug())

# Detach the previously attached DeLorean data frame
detach(dl)


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DeLorean documentation built on May 2, 2019, 9:24 a.m.