Skip to content

ggNetView_RMT找不到对象'SparCC_graph' #7

@PHON1105

Description

@PHON1105

您好,我(R版本4.5.2)使用示例数据otu_rare_relative.rda运行函数ggNetView_RMT时返回错误“找不到对象'SparCC_graph'”。查阅了您提供的ggNetView_RMT.R发现,第149行至第154行的变量SparCC_graph未被定义?同时留意到build_graph_from_mat.R中的第198行:# SparCC_graph <- abs(SparCC_obj$Cor) >= r.threshold。这两者是否有关?请您指教!感谢><
我运行的代码如下:

我对示例数据进行了丰度过滤
filter_thres <- 0.0005
avg_rel_abund <- rowMeans(otu_rare_relative)
otu_rare_relative2 <- otu_rare_relative[avg_rel_abund > filter_thres, ]

out <- ggNetView_RMT(
   mat = otu_rare_relative2,
   transfrom.method ="log10",
   method ="SparCC",
   cor.method ="spearman",
   unfold.method ="gaussian",
   bandwidth ="nrd0",
   nr.fit.points = 51,
   discard.outliers = TRUE,
   discard.zeros = TRUE,
   min.mat.dim = 40,
   max.ev.spacing = 3,
   save_plots = FALSE,
   out_dir ="RMT_plots",
   verbose = TRUE,
   seed = 1115 )
错误: 找不到对象'SparCC_graph'

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions