Error in runUMAP(Similarity, min.dist = 0.3, n.neighbors = k)

[Emily-Y21]

I have a problem when running:

cellchat <- netEmbedding(cellchat, type = "functional")

Manifold learning of the signaling networks for a single dataset 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')).

I have used reticulate::py_install(packages = 'umap-learn') to install 'umap-learn',but it can't help. I tried to library(umap-learn) after installation, but it shows: Error in library(umap - learn) : The length of 'package' must be one

Can you kindly help me with this problem? Thank you very much!

[sqjin]

@Emily-Y21 You might need to specify the python version, e.g., reticulate::use_python("/Users/USERS/opt/miniconda3/bin/python", required=T)

[Emily-Y21]

Thanks for your answer.But it still has something wrong. I use the following code to install 'umap-learn'.

remotes::install_github("hafen/rminiconda") py <- rminiconda::find_miniconda_python("my_python") reticulate::use_python(py, required = TRUE) reticulate::py_install(packages = 'umap-learn')

but when I run > cellchat <- netEmbedding(cellchat, type = "functional") it still returns an error

------------------ 原始邮件 ------------------ 发件人: "sqjin/CellChat" @.>; 发送时间: 2021年3月18日(星期四) 上午6:42 @.>; @.**@.>; 主题: Re: [sqjin/CellChat] Error in runUMAP(Similarity, min.dist = 0.3, n.neighbors = k) (#158)

@Emily-Y21 You might need to specify the python version, e.g., reticulate::use_python("/Users/USERS/opt/miniconda3/bin/python", required=T)

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[sqjin]

@Emily-Y21 Can you please check https://github.com/lmcinnes/umap to see how to run umap in R?

[yujuan-53]

hello,would you solve this question?now, I meet same problem

[apal6]

Hi,

Thank you for the wonderful package. I wonder if this problem was solved as I encountered the same error.

Best, Aastha