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taowenmicro / ggClusterNet

Microbial ecological network visualization clustering
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Sample data (ps) is not running #2

Open Yichel518 opened 2 years ago

Yichel518 commented 2 years ago

Hello! I met a trouble when I run

data(ps) result = network(ps = ps,N = 0.001,r.threshold=0.6,p.threshold=0.05,label = FALSE,path = path ,zipi = TRUE) Error in validObject(.Object) : invalid class “otu_table” object: OTU abundance data must have non-zero dimensions." And then using my own data the same error occurs, and after I have replaced the relative abundance with a count file, the structure of my object looks like this data phyloseq-class experiment-level object otu_table() OTU Table: [ 17 taxa and 38 samples ] sample_data() Sample Data: [ 38 samples by 4 sample variables ] tax_table() Taxonomy Table: [ 17 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 17 tips and 16 internal nodes ]

what is wrong with my codes?

xph007 commented 2 years ago

Thank you for your support "ggClusterNet". The error was caused by the wrong parameter "N = 0.001".  "N=integer", it meas extract  the top N number relative abundance of OTU.

------------------ 原始邮件 ------------------ 发件人: "taowenmicro/ggClusterNet" @.>; 发送时间: 2022年3月12日(星期六) 晚上11:31 @.>; @.***>; 主题: [taowenmicro/ggClusterNet] Sample data (ps) is not running (Issue #2)

Hello! I met a trouble when I run

data(ps) result = network(ps = ps,N = 0.001,r.threshold=0.6,p.threshold=0.05,label = FALSE,path = path ,zipi = TRUE) Error in validObject(.Object) : invalid class “otu_table” object: OTU abundance data must have non-zero dimensions." And then using my own data the same error occurs, and after I have replaced the relative abundance with a count file, the structure of my object looks like this data phyloseq-class experiment-level object otu_table() OTU Table: [ 17 taxa and 38 samples ] sample_data() Sample Data: [ 38 samples by 4 sample variables ] tax_table() Taxonomy Table: [ 17 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 17 tips and 16 internal nodes ]

what is wrong with my codes?

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taowenmicro commented 2 years ago

文档：ggClusterNet-保姆级教程.md 链接：http://note.youdao.com/noteshare?id=c8c1e6f906470a3765f3cf514b204679