宏基因组,物种进化树LDA,lefse

仿生bug

于 2025-01-04 21:49:50 发布

阅读量171

点赞数 1

文章标签： r语言流行病学宏基因组

本文链接：https://blog.youkuaiyun.com/weixin_46623488/article/details/144935752

版权

library(microbiome)
dataset

dataset$sample_table <- dataset$sample_table[1:45,]
tax_table <- dataset$tax_table[1:45,]


dataset <- microtable$new(sample_table = dataset$sample_table, 
                          otu_table = dataset$otu_table[1:45,],
                          tax_table = tax_table)
dataset$tidy_dataset()

lefse <- trans_diff$new(dataset = dataset,method = "lefse",
                        alpha = 0.01, group ="Group", 
                        lefse_subgroup = NULL)
lefse$plot_diff_cladogram(use_taxa_num = 200,  
                          use_feature_num = 50, 
                          clade_label_level = 4)
# we show 20 taxa with the highest LDA (log10)
lefse$plot_diff_bar(use_number = 1:10,
                    width = 0.8)