Question

how to plot a fitting line on the testPseudotime

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Guandong Shang ▴ 40

@shangguandong1996-21805

Last seen 2.0 years ago

China

Hi, I run the testPseudotime() according to the OSCA Changes along a trajectory. and I also plot the logExpression-Pseudotime plot.

But I am wondering whether I can fit a line for the plotExpression plot like below. Or I just use the geom_smooth to fit.

enter image description here

Best wishes

Guandong Shang

Pseudotime testPseudotime TSCAN SingleCell OSCA • 1.3k views

ADD COMMENT • link 2.2 years ago Guandong Shang ▴ 40

score 0 · Answer 1 · 2022-09-12

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Aaron Lun ★ 28k

@alun

Last seen just now

The city by the bay

plotExpression just returns a ggplot object, so you should be able to add further custom layers on top using standard ggplot2 methods.

Alternatively, tradeSeq probably has some suitable visualization methods that you could look at.

ADD COMMENT • link 2.2 years ago Aaron Lun ★ 28k

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Hi, Aaron. I just wondering whehter I should choose suitable model to plot the fit line. Just as you say in OSCA

We use the testPseudotime() utility to fit a natural spline to the expression of each gene, allowing us to model a range of non-linear relationships in the data.

Should I plot a line that capture the non-linear relationship from the testPseudotime() ?