1 微生物组数据使用TMM等矫正测序数据-更加适合目前发文章要求
2 使用箱线图可视化距离矩阵
library(tidyverse)
library(ggClusterNet)
library(phyloseq)
data(ps)
ps.scale = scale_micro(ps,method = "TMM" )
unif <- phyloseq::distance(ps.scale , method= "bray") %>%
as.matrix()
gro = sample_data(ps)
head(gro)
library(tidyfst)
dat1 = unif %>%
as.matrix() %>%
tidyfst::mat_df()
head(dat1)
A = c()
for (i in 1:dim(dat1)[1]) {
if (gro[dat1$row[i],][[2]] == gro[dat1$col[i],][[2]]) {
A[i] = T
} else {
A[i] =F
}
}
dat1$group = A
head(gro)
gro$id = row.names(gro)
dat2 = dat1 %>% filter(group == T) %>%
left_join(gro,by = c("row" = "id"))
head(dat2)
ggplot(dat2) +
geom_boxplot(aes(x = Group,y = value,color =Group,fill = Group),alpha = 0.3) +
theme_classic()