Footsteps on my way !

# cellchat netEmbedding 运行出错

Error in runUMAP(Similarity, min.dist = 0.3, n.neighbors = k) : Cannot find UMAP, please install through pip (e.g. pip install umap-learn or reticulate::py_install(packages = 'umap-learn')).

library(reticulate)
use_python('/usr/bin/python3',required = T) #指定安装umap-learn那个版本的python位置
py_version() #看看是不是指定正确

>cellchat <- netEmbedding(cellchat, type = "functional")
Manifold learning of the signaling networks for a single dataset
/Users/yangl/Library/Python/3.8/lib/python/site-packages/umap/umap_.py:132: UserWarning: A large number of your vertices were disconnected from the manifold.
Disconnection_distance = 1 has removed 142 edges.
It has fully disconnected 3 vertices. You might consider using find_disconnected_points() to find and remove these points from your data.
Use umap.utils.disconnected_vertices() to identify them.
warn(

>cellchat <- netEmbedding(cellchat, type = "functional")
Manifold learning of the signaling networks for a single dataset
C:\Users\zzu\AppData\Local\R-MINI~1\envs\R-RETI~1\lib\site-packages\umap\umap_.py:133: UserWarning: A large number of your vertices were disconnected from the manifold.
Disconnection_distance = 1 has removed 142 edges.
It has fully disconnected 3 vertices.
You might consider using find_disconnected_points() to find and remove these points from your data.
Use umap.utils.disconnected_vertices() to identify them.
f"A large number of your vertices were disconnected from the manifold.\n"

install.packages("uwot")
library(uwot)
cellchat <- netEmbedding(cellchat, umap.method = 'uwot',type = "functional") #调用uwot实现umap, 程序自带，只需使用参数umap.method = 'uwot'，无需修改对应的netEmbedding函数源码