kandi X-RAY | monocle-release Summary
kandi X-RAY | monocle-release Summary
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QUESTION
I have managed to generate pseudotime vs gene expression plots in Monocle for individual markers using the following code:
...ANSWER
Answered 2020-Feb-12 at 16:47You can access the Pseudotime and "expectation"
values that comprise the curve in plot$data
(monocle just plots Pseudotime against spline-smoothed mean expression for the specified genes).
You can then use approxfun
to do 2d interpolation and evaluate a grid of points along the range of pseudotime.
NOTE: I am not sure this is a sensible thing to do. Pseudotime is a fairly loose and wooly thing, and reading deeply into minute changes in pseudotime is likely to lead to pretty shaky conclusions.
In any case, if you're interested in using this type of approach I would just read the code on github as it should be fairly easy to reproduce the output.
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