Beta多样性可视化

最后发布时间 : 2022-11-04 13:02:51 浏览量 :

主坐标分析PCoA

SampleID	Group
KO1	KO
KO2	KO
KO3	KO
KO4	KO
KO5	KO
KO6	KO

metadata

bray_curtis	KO1	KO2	KO3	KO4	KO5	KO6	OE1	OE2	OE3	OE4	OE5	OE6	WT1	WT2	WT3	WT4	WT5	WT6
KO1	0	0.309	0.338	0.302	0.339	0.277	0.33	0.357	0.333	0.311	0.289	0.307	0.313	0.337	0.31	0.319	0.335	0.308
KO2	0.309	0	0.374	0.36	0.436	0.322	0.322	0.332	0.341	0.338	0.297	0.321	0.307	0.351	0.298	0.299	0.353	0.313
KO3	0.338	0.374	0	0.336	0.339	0.346	0.427	0.415	0.375	0.368	0.361	0.412	0.387	0.37	0.38	0.362	0.359	0.338
KO4	0.302	0.36	0.336	0	0.341	0.283	0.405	0.412	0.375	0.352	0.345	0.393	0.344	0.343	0.369	0.36	0.356	0.347
KO5	0.339	0.436	0.339	0.341	0	0.339	0.475	0.448	0.44	0.404	0.392	0.463	0.396	0.367	0.414	0.413	0.371	0.384
KO6	0.277	0.322	0.346	0.283	0.339	0	0.38	0.41	0.37	0.339	0.32	0.359	0.347	0.354	0.355	0.345	0.347	0.353

bray_curtis

suppressWarnings(suppressMessages(library(amplicon)))
suppressMessages(library(tidyverse))
distance_mat = read.table("https://gitee.com/bioinfoFungi/amplicon/raw/master/results/beta/bray_curtis.txt", header=T, row.names=1, sep="\t", comment.char="", stringsAsFactors = F)
metadata = read.table("https://gitee.com/bioinfoFungi/amplicon/raw/master/data/metadata.txt", header=T, row.names=1, sep="\t", comment.char="", stringsAsFactors = F)
beta_pcoa(distance_mat, metadata, groupID = "Group", label=T)

图片alt

Alpha多样性可视化物种组成可视化