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duct317 / scDHA

A tool for single-cell data analysis.
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about pseudo-time inference #14

Closed nbnbhwyy closed 1 year ago

nbnbhwyy commented 1 year ago

Dear scDHA authors,

Thank you for your great work! I would like to ask about the pseudo-timing inference related to Figure 3. Unlike in the figure, in the implementation provided by the author (R package), cells of the same type are located in the same y-axis. Is there a random perturbation added. Also, did the author draw the curve in Figure 3(a) by hand, or did he get it from some package? Could you please help me with this issue?

nbnbhwyy commented 1 year ago

The author emailed me a reply and I'm posting it here.

Hi, For the figure 3a, you can generate the curve by fitting the x and y coordinate of points (sorted by time) to a curve using R's loess function.

https://statisticsglobe.com/fit-smooth-curve-to-plot-of-data-in-r

For figure 3b, the figure in the paper was generated using ggplot2's geom_jitter function instead of the R's boxplot function as in the package vignette.

https://ggplot2.tidyverse.org/reference/geom_jitter.html

And, as Dr. Nguyen mentioned, all the code used to generate the figures in the paper would be included in the docker available here:

https://bioinformatics.cse.unr.edu/software/scDHA/resource/Reproducibility/ Yours sincerely,

Duc.