how to find root_node value

[Yumy526]

Dear CAPITAL developers, hello,What does root_node value represent please? How to determine that? I didn't find the relevant information. I tried the following sentence

cp.tl.trajectory_tree(adata1, root_node="10", groupby="idents", tree=None) the error: myident:

I don't know why it's wrong

please help me

[Rsugihara01]

Hi @Yumy526,

The root node is a cluster where cell differentiation starts in that cell group. To determine that, you need to do some basic analysis (clustering and gene expression analysis etc. ) like scanpy tutorials.

The problem seems to be that you're trying to use a string “10” to specify 'indents,' which is stored as an integer 10.

Can you try

cp.tl.trajectory_tree(adata1, root_node=10, groupby="idents", tree=None)

or change the int to string using

adata = adata.obs[“indents”].astype(str)

Hope this solves the problem!

Rsugihara01

[Yumy526]

It is my  pleasure to receive your reply.  I encountered a error, limited ability, sorry to disturb you again.I really don't know why this problem is happening  Here's my error：

But I have a guess if there is a problem with the preprocessing step：

陪我吹吹风 @.***

Such a problem arises when preprocessing of Caplital is carried out（One thing to add: I have standardized my data myself in advance，I wonder if it's because raw data is needed） 

My thirst for knowledge makes me eager to get your reply Looking forward to hearing from you. Thank you so much

------------------ 原始邮件 ------------------ 发件人: "ykat0/capital" @.>; 发送时间: 2023年8月9日(星期三) 中午11:37 @.>; @.**@.>; 主题: Re: [ykat0/capital] how to find root_node value (Issue #5)

Hi @Yumy526,

The root node is a cluster where cell differentiation starts in that cell group. To determine that, you need to do some basic analysis (clustering and gene expression analysis etc. ) like scanpy tutorials.

The problem seems to be that you're trying to use a string “10” to specify 'indents,' which is stored as an integer 10.

Can you try

cp.tl.trajectory_tree(adata1, root_node=10, groupby="idents", tree=None)

or change the int to string using

adata = adata.obs[“indents”].astype(str)

Hope this solves the problem!

Rsugihara01

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