物种组成可视化

最后发布时间 : 2022-11-05 09:58:46 浏览量 :

堆叠柱状图Stackplot

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

metadata

Phylum	KO1	KO2	KO3	KO4	KO5	KO6	OE1	OE2	OE3	OE4	OE5	OE6	WT1	WT2	WT3	WT4	WT5	WT6	All
Proteobacteria	65.9	51.6	62.4	63	74.8	70	57.5	48.2	51	56.9	59.5	57.3	51.6	61.2	57.4	56.7	57	57.8	53.9
Actinobacteria	26.5	40.3	27.7	28.7	17.4	24.3	29.5	36	34.2	29.1	31	29.7	36.1	30	32.5	34.5	34.8	32	28.5
Bacteroidetes	3.03	2.67	7.29	3.05	4.75	2.12	3.62	8.07	8.71	7.4	3.72	3.53	5.36	6.03	4.7	4.11	4.83	5.75	5
Firmicutes	1.74	1.96	1.22	3.23	0.73	1.52	5.19	2.81	2.56	3.37	1.79	5.2	0.82	0.62	1.22	1.02	0.53	1.11	3.9
Chloroflexi	1.85	2.43	0.63	1.38	1.56	1.2	1.64	3.03	1.7	1.88	2.12	1.93	4.76	0.99	1.87	2.04	2.01	2.1	3.7
Acidobacteria	0.3	0.34	0.19	0.13	0.22	0.27	0.95	0.41	0.55	0.27	0.72	0.84	0.33	0.34	0.92	0.46	0.13	0.33	1.4

sum_p

suppressWarnings(suppressMessages(library(amplicon)))
suppressMessages(library(tidyverse))
library(RColorBrewer)
metadata = read.table("https://gitee.com/bioinfoFungi/amplicon/raw/master/data/metadata.txt", header=T, row.names=1, sep="\t", comment.char="", stringsAsFactors = F)
taxonomy = read.table("https://gitee.com/bioinfoFungi/amplicon/raw/master/results/tax/sum_p.txt", header=T, row.names=1, sep="\t", comment.char="", quote = "")
p = tax_stackplot(taxonomy, metadata, topN = 7, groupID = "Group", style = "group", sorted = "abundance")
p + scale_fill_brewer(palette = "Paired")

弦/圈图circlize

suppressWarnings(suppressMessages(library(amplicon)))
metadata = read.table("https://gitee.com/bioinfoFungi/amplicon/raw/master/data/metadata.txt", header=T, row.names=1, sep="\t", comment.char="", stringsAsFactors = F)
taxonomy = read.table("https://gitee.com/bioinfoFungi/amplicon/raw/master/results/tax/sum_p.txt", header=T, row.names=1, sep="\t", comment.char="", quote = "")
tax_circlize(taxonomy, metadata, topN = 4, groupID = "Group")

树图treemap

Beta多样性可视化物种组成差异分析可视化