库由ggplot2和phyoloseq组成 数据= Globalpatterns
GP = filter_taxa(GlobalPatterns, function(x) sum(x > 3) > (0.2*length(x)), TRUE)
GP = filter_taxa(GlobalPatterns, function(x) sum(x > 3) > (0.2*length(x)), TRUE)
定义人类与非人类分类变量，并将此新变量添加到样本数据中：
sample_data(GP)$human = factor( get_variable(GP, "SampleType") %in% c("Feces", "Mock", "Skin", "Tongue")）
将丰度标准化为中值测序深度
total = median(sample_sums(GP))
standf = function(x, t=total) round(t * (x / sum(x)))
gps = transform_sample_counts(GP, standf)
使用3.0的截止值对变异系数
过滤分类单元gpsf = filter_taxa(gps, function(x) sd(x)/mean(x) > 3.0, TRUE)
Subset the data to Bacteroidetes, used in some plots
gpsfb = subset_taxa(gpsf, Phylum=="Bacteroidetes")
绘制数据
title = "plot_bar; Bacteroidetes-only"
plot_bar(gpsfb, "SampleType", "Abundance", title=title)
问题：我需要编写哪些代码，用当前的例子来测试特定样本类型（如粪便）的拟杆菌的丰度差异？