(R语言微生物统计)NDMS(6海岛样本菌落组成差异分析).docx

NDMS(6海岛样本菌落组成差异分析）
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同时考虑g样本间距离，也考虑了样本距离以及物种（OTU）在各样本中的分布，由于参与排序的物种（OTU）种类过多不便全部展示，最终选择展示相对丰度前10的OTU。对6种海岛分组，在作图结果中分别以不同颜色和不同形状的点表示出各个海岛的样品分布，而主要的OTU，在图中对应的坐标位置直接展示其名称。
library(vegan)
## Loading required package: permute
## Loading required package: lattice
## This is vegan -6
library(ggplot2)
#读入 OTU 丰度表
otu <- ('', = 1, sep = '\t', stringsAsFactors = FALSE, = FALSE)
otu <- (t(otu))
#读入样本分组文件
group <- ('', sep = '\t', stringsAsFactors = FALSE)
#排序，预设 2 个排序轴
nmds1 <- metaMDS(otu, distance = 'bray', k = 2)
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.
## Run 1 stress 0.
## ... New best solution
## ... Procrustes: rmse 0. max resid 0.
## Run 2 stress 0.
## ... New best solution
## ... Procrustes: rmse 0. max resid 0.
## Run 3 stress 0.
## ... Procrustes: rmse 0. max resid 0.
## Run 4 stress 0.
## ... New best solution
## ... Procrustes: rmse 0. max resid 0.
## Run 5 stress 0.
## ... New best solution
## ... Procrustes: rmse 0. max resid 0.
## Run 6 stress 0.
## ... New best solution
## ... Procrustes: rmse 0. max resid 0.
## Run 7 stress 0.
## ... New best solution
## ... Procrustes: rmse 0. max resid 0.
## Run 8 stress 0.
## Run 9 stress 0.
## Run 10 stress 0.
## Run 11 stress 0.
##