search

XingyanLiu / stagewiseNN

Constructing a developmental tree from scRNA-seq data
https://XingyanLiu.github.io/stagewiseNN/index.html
MIT License
1 stars 1 forks source link

tutorial of edgedf.csv and ggtree #2

Closed grimwoo closed 2 years ago

grimwoo commented 2 years ago

hi , thanks for the development of stagewiseNN.

Using the provided "subsampled_B-L0-0.2.h5ad" and the detailed tutorial, I successfully got the "edgedf.csv" file. Could I know the following tutorial to plot the tree in ggtree with the "edgedf.csv" ?

image

XingyanLiu commented 2 years ago

The developmental tree is plotted by the R package 'ggtree' (https://github.com/YuLab-SMU/ggtree). The codes/tutorial for plotting the figures in the CR paper will be complemented later this week.

grimwoo commented 2 years ago

@XingyanLiu Thank you for your quick reply and look forward to your code this week~

XingyanLiu commented 2 years ago

The function for visualizing the developmental tree can be found at https://github.com/XingyanLiu/AmphioxusAnalysis

image
grimwoo commented 2 years ago

@XingyanLiu Thank you so much