导读
Bary-Curtis PCoA降维分析菌群结构。
一、输入数据
1.1 菌属丰度矩阵
df = data.frame(abs(round(matrix(rnorm(729, 100, 50), 27, 27))))
rownames(df) = paste(rep(paste(rep(c("A", "B", "C"), each=3), rep(c("I","II","III")), sep=""), each=3), 1:3, sep="")
colnames(df) = paste("genus", 1:27, sep="")
1.2 样品分组
df_group = paste(rep(c("A", "B", "C"), each=9), rep(c("I","II","III"), each=3), sep="")
data.frame(rownames(df), df_group)
二、BC PCoA函数
library(vegan)
library(ggplot2)
library(ape)
pcoa_f = function(input, group)
{
pcoa = pcoa(vegdist(input, method = "bray"))
pcoa_point = data.frame(pcoa$vectors[, c(1, 2)], Category = group)
pcoa_point$Group = substring(pcoa_point[, 3], 1, 1)
pcoa_point$Mark = substring(pcoa_point[, 3], 2)
write.csv(pcoa_point, file="bray_curtis_pcoa.csv")
xylab = paste(c("Axis.1 [", "Axis.2 ["), round(pcoa$values$Relative_eig[1:2]*100, 2), "%]", sep = "")
result = ggplot(pcoa_point, aes(x=Axis.1, y=Axis.2, color = Group)) +
geom_point(aes(shape = Mark), size = 4) +
stat_ellipse(level = 0.95, show.legend = F, aes(fill = Category)) +
theme_classic() +
labs(x=xylab[1], y=xylab[2], title = paste('Bray-Curtis PCoA')) +
scale_color_manual(values=c("A" = "#EE6363", "B" = "#1E90FF", "C" = "#00C5CD")) +
guides(color = guide_legend(order=1), shape = guide_legend(order=2))
ggsave(result, filename="bray_curtis_pcoa.pdf")
}
三、分析及结果
pcoa_f(df, df_group)
ellipse出错，圈圈没有出来，模拟数据效果不好
3.1 结果文件
3.2 结果表
3.3 结果图
四、实际分析举例图
一组bray curtis pcoa参数
ggplot(pcoa_point, aes(x=Axis.1, y=Axis.2, fill=source)) +
geom_point(pch=21, size=7, color="white") +
stat_ellipse(level = 0.95, show.legend = F,
aes(color=source), size = 1) +
theme_classic() +
labs(x=xylab[1], y=xylab[2],
title = paste('Bray-Curtis PCoA'),
fill = "Source") +
theme(title = element_text(size = 15, face="bold")) +
theme(legend.text=element_text(size=15)) +
theme(legend.title=element_text(face='bold', size=20)) +
theme(axis.title = element_text(size = 20)) +
theme(axis.text = element_text(size = 20),
axis.line = element_line(size = 1.2),
axis.ticks = element_line(size = 1.2)) +
theme(plot.title = element_text(face="bold", size=16)) +
scale_fill_manual(
values = c("Colon"="#00BA38",
"Stool"="#F8766D",
"Ileum"="#619CFF")) +
scale_color_manual(
values = c("Colon"="#00BA38",
"Stool"="#F8766D",
"Ileum"="#619CFF"))
更多参数
library("ggalt")
geom_encircle(aes(group = Group, colour = Group)) # 外点连线
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