GMSB文章六：微生物SCFA关联分析

于 2024-06-27 17:38:50 发布
阅读量659 收藏 25
点赞数 9
分类专栏： 复现文章 文章标签： 数据分析 r语言
版权声明：本文为博主原创文章，遵循 CC 4.0 BY-SA 版权协议，转载请附上原文出处链接和本声明。
本文链接：https://blog.csdn.net/H20230717/article/details/140019519
版权

欢迎大家关注全网生信学习者系列：

  • WX公zhong号：生信学习者
  • Xiao hong书：生信学习者
  • 知hu：生信学习者
  • CDSN：生信学习者2

介绍

微生物短链脂肪酸（SCFAs）是由肠道微生物发酵膳食纤维、抗性淀粉、低聚糖等碳水化合物产生的一类有机脂肪酸，主要包括乙酸、丙酸和丁酸。SCFAs在肠道健康、免疫调节、能量代谢等方面发挥重要作用，并且与多种疾病状态有关。

通过约束线性混合效应模型（CLME）研究SCFA与排序暴露分组之间的单调递增关系，这种方法通常用于分析具有层次结构的数据，能够处理数据中的非独立性和非正态分布问题。在研究SCFA与某些因素（如饮食、疾病状态等）的关系时，CLME可以用来评估这些因素对SCFA水平的影响，并检测它们之间是否存在单调递增或递减的关系。

加载R包

library(readr)
library(tidyverse) 
library(CLME)
library(magrittr)
library(qwraps2)
library(ggprism)
library(ggsci)
library(ggpubr)
library(rstatix)
library(jtools)
library(kableExtra)

导入数据

大家通过以下链接下载数据：

  • 百度网盘链接：https://pan.baidu.com/s/1fz5tWy4mpJ7nd6C260abtg
  • 提取码: 请关注WX公zhong号_生信学习者_后台发送 复现gmsb 获取提取码
df_merge <- read_csv("./data/GMSB-data/df_merge.csv", show_col_types = FALSE)

head(df_merge[, 1:6])
sampleidsubjidvisitvisit_numstatusage
F-1DUMMY1v110nc58
F-2DUMMY2v110nc60
F-3DUMMY3v110nc58
F-4DUMMY4v110nc72
F-5DUMMY5v110nc57
F-6DUMMY6v110nc59

数据预处理

对不同visit进行分组中，提取它们的SCFA短链脂肪酸

df_v1 <- df_merge %>%
  dplyr::filter(visit == "v1",
         group1 != "missing")
df_v2 <- df_merge %>%
  dplyr::filter(visit == "v2",
         group1 != "missing")

df_v1$group1 <- recode(df_v1$group1,
                      `g1` = "G1", `g2` = "G2",
                      `g3` = "G3", `g4` = "G4")
df_v1$group2 <- recode(df_v1$group2,
                      `g1` = "G1", `g2` = "G2",
                      `g3` = "G3", `g4` = "G4", `g5` = "G5")

df_v1 <- df_v1 %>%
  dplyr::transmute(subjid, status, leu3p, leu2p, recept_anal, abx_use, group1, group2, 
            acetate_v1 = acetate, propionate_v1 = propionate, 
            butyrate_v1 = butyrate, valerate_v1 = valerate)
df_v2 <- df_v2 %>%
  dplyr::transmute(subjid, 
            acetate_v2 = acetate, propionate_v2 = propionate, 
            butyrate_v2 = butyrate, valerate_v2 = valerate) 

df_v1 <- df_v1 %>%
  dplyr::left_join(df_v2, by = "subjid")

df_v1$group1 <- factor(df_v1$group1, levels = c("G1", "G2", "G3", "G4"), ordered = TRUE)
df_v1$group2 <- factor(df_v1$group2, levels = c("G1", "G2", "G3", "G4", "G5"), ordered = TRUE)

head(df_v1[, 1:6])
subjidstatusleu3pleu2precept_analabx_use
DUMMY1nc40.535.95yes
DUMMY2nc53.927.76yes
DUMMY3nc30.942.53no
DUMMY4nc50.319.37no
DUMMY5nc42.838.84no
DUMMY6nc36.946.74yes

visit1

visit1群体的SCFA的数据分布情况

df_v1 %>% 
  dplyr::select(acetate_v1, propionate_v1, butyrate_v1, valerate_v1) %>%
  pastecs::stat.desc() %>% 
  kable() %>% 
  kable_styling()

在这里插入图片描述

结果：不同的SCFA的数据描述结果，比如acetate_v1最大和最小值都要高于其他的。

visit2

visit2群体的SCFA的数据分布情况

df_v1 %>% 
  dplyr::select(acetate_v2, propionate_v2, butyrate_v2, valerate_v2) %>%
  pastecs::stat.desc() %>% 
  kable() %>% 
  kable_styling()

在这里插入图片描述

结果：不同的SCFA的数据描述结果，比如acetate_v1最大和最小值都要高于其他的。

SCFA ~ groups: box plots

线性回归校正abx_use因素比较不同分组的差异

plot_box <- function(
    group_lab, group_var, 
    key_var, title, 
    y.position, step.increase) {
  
  df_fig <- df_v1 %>%
    transmute(group = get(group_var), value = get(key_var), abx_use)
  df_fig$group <- factor(df_fig$group, ordered = FALSE)
  lm_fit <- lm(value ~ group + abx_use, data = df_fig)
  df_p <- data.frame(group1 = group_lab[1],
                    group2 = group_lab[-1],
                    p = summary(lm_fit)$coef[grepl("group", names(coef(lm_fit))), "Pr(>|t|)"]) %>%
    mutate(p = round(p, 2))
  
  bxp <- ggboxplot(df_fig, x = "group", y = "value", color = "group",
                  add = "jitter", 
                  xlab = FALSE, ylab = FALSE, title = title) +
    stat_pvalue_manual(df_p, y.position = y.position, 
                       step.increase = step.increase, label = "p") +
    scale_color_npg(name = "Group") +
    theme(axis.text.x = element_blank(),
          axis.ticks.x = element_blank(),
          strip.background = element_rect(fill = "white"),
          legend.position = "bottom",
          plot.title = element_text(hjust = 0.5))
  
  return(bxp)
}

Primary group

Primary group: 按照频率分组

  • G1: # receptive anal intercourse = 0

  • G2: # receptive anal intercourse = 1

  • G3: # receptive anal intercourse = 2 - 5

  • G4: # receptive anal intercourse = 6 +

bxp_list <- list()
var_list <- c("acetate_v1", "butyrate_v1", "propionate_v1", "valerate_v1")
title_list <- c("Acetate", "Butyrate", "Propionate", "Valerate")
y_pos_list <- c(6, 0.25, 0.35, 0.07)
step_list <- c(0.1, 0.1, 0.1, 0.1)

for (i in seq_along(var_list)) {
  bxp <- plot_box(group_lab = c("G1", "G2", "G3", "G4"),
                 group_var = "group1",
                 key_var = var_list[i], title = title_list[i],
                 y.position = y_pos_list[i], step.increase = step_list[i])
  bxp_list[[i]] <- bxp
}

ggarrange(
  bxp_list[[1]], bxp_list[[2]], 
  bxp_list[[3]], bxp_list[[4]],
  common.legend = TRUE)

在这里插入图片描述

结果：上述短链脂肪酸在分组间均不存在显著差异。

Secondary group

Secondary group: 按照频率分组2

  • G1: # receptive anal intercourse = 0

  • G2: # receptive anal intercourse = 1

  • G3: # receptive anal intercourse = 2 - 3

  • G4: # receptive anal intercourse = 4 - 8

  • G5: # receptive anal intercourse = 9 +

bxp_list <- list()
var_list <- c("acetate_v1", "butyrate_v1", "propionate_v1", "valerate_v1")
title_list <- c("Acetate", "Butyrate", "Propionate", "Valerate")
y_pos_list <- c(6, 0.25, 0.35, 0.07)
step_list <- c(0.1, 0.1, 0.1, 0.1)

for (i in seq_along(var_list)) {
  bxp <- plot_box(group_lab = c("G1", "G2", "G3", "G4", "G5"),
                 group_var = "group2",
                 key_var = var_list[i], title = title_list[i],
                 y.position = y_pos_list[i], step.increase = step_list[i])
  bxp_list[[i]] <- bxp
}

ggarrange(
  bxp_list[[1]], bxp_list[[2]], 
  bxp_list[[3]], bxp_list[[4]],
  common.legend = TRUE)

在这里插入图片描述

结果：短链脂肪酸在分组间的分布。

  • Acetate在G1和G5间显著差异；

  • Valerate在G1和G5间显著差异

SCFA ~ groups: increasing trend

约束线性混合效应模型（CLME, Constrained Linear Mixed Effects Models）：用于评估性暴露组和血浆炎症细胞因子水平之间的单调递增趋势，同时校正细菌抗生素使用情况。

  • plot_clme用于绘制趋势图
plot_clme <- function(
    clme_obj, 
    group, 
    y_min, y_max, 
    p_gap, 
    ann_pos, 
    trend = "increase", 
    ...) {
  
  overall_p <- clme_obj$p.value
  ind_p <- clme_obj$p.value.ind
  est_mean <- clme_obj$theta[group]
  est_se <- sqrt(diag(clme_obj$cov.theta))[group]
  
  df_fig <- data.frame(x = group, y = est_mean, err = est_se)
  
  if (est_mean[2] < est_mean[length(est_mean)]) {
    start_p_pos <- est_mean[2] + p_gap
    end_p_pos <- max(est_mean) + p_gap
  } else if (est_mean[2] > est_mean[length(est_mean)]) {
    start_p_pos <- max(est_mean) + p_gap
    end_p_pos <- min(est_mean) + p_gap
  } else {
    if (trend == "increase") {
      start_p_pos <- est_mean[2] + p_gap
      end_p_pos <- max(est_mean) + 2 * p_gap
    } else {
      start_p_pos <- max(est_mean) + 2 * p_gap
      end_p_pos <- min(est_mean) + p_gap
    }
  }
  
  df_p <- data.frame(group1 = group[seq_len(length(group) - 1)],
                    group2 = group[-1],
                    x = group[-1],
                    label = paste0("p = ", round(ind_p, 3)),
                    y.position = seq.int(from = start_p_pos, 
                                         to = end_p_pos, 
                                         length.out = length(group) - 1))
  df_ann <- data.frame(x = group[1], y = ann_pos,
                      fill = "white",
                      label = paste0("Trend p-value = ", round(overall_p, 3)))
  
  fig <- df_fig %>%
    ggplot(aes(x = x, y = y)) +
    geom_bar(stat = "identity", color = "black", aes(fill = x)) + 
    geom_errorbar(aes(ymin = y - 1.96 * err, ymax = y + 1.96 * err), 
                  width = .2, position = position_dodge(.9)) +
    add_pvalue(df_p,
               xmin = "group1",
               xmax = "group2",
               label = "label",
               y.position = "y.position",
               remove.bracket = FALSE, 
               ...) +
    geom_label(data = df_ann, aes(x = x, y = y, label = label), 
               size = 4, vjust = -0.5, hjust = 0, color = "black") +
    ylim(y_min, y_max) +
    theme_bw()
  
  return(fig)
}

  1. P-value is obtained by linear regression adjusting for antibiotics usage.

  2. P-values were not adjusted for multiple comparisons.

限制参数

cons <- list(order = "simple", decreasing = FALSE, node = 1)

Primary grouping: Acetate

短链脂肪酸Acetate与Primary grouping的相关关系

fit1 <- clme(acetate_v1 ~ group1 + abx_use, data = df_v1, constraints = cons, seed = 123)
summ_fit1 <- summary(fit1)

fig_ace_primary <- plot_clme(
    summ_fit1, 
    group = c("G1", "G2", "G3", "G4"), 
    y_min = 0, y_max = 4, 
    p_gap = 0.7, ann_pos = 3.5) +
  scale_fill_npg(name = NULL) +
  labs(x = NULL, y = "Acetate")

fig_ace_primary

在这里插入图片描述

结果：acetate在不同组有显著差异的单调递增的趋势（G3和G4组存在显著差异）。

Primary grouping: Butyrate

短链脂肪酸Butyrate与Primary grouping的相关关系

fit2 <- clme(butyrate_v1 ~ group1 + abx_use, data = df_v1, constraints = cons, seed = 123)
summ_fit2 <- summary(fit2)

fig_but_primary <- plot_clme(
    summ_fit2, 
    group = c("G1", "G2", "G3", "G4"), 
    y_min = 0, y_max = 0.18, 
    p_gap = 0.04, ann_pos = 0.16) +
  scale_fill_npg(name = NULL) +
  labs(x = NULL, y = "Butyrate")

fig_but_primary

在这里插入图片描述

Primary grouping: Propionate

短链脂肪酸Propionate与Primary grouping的相关关系

fit3 <- clme(propionate_v1 ~ group1 + abx_use, data = df_v1, constraints = cons, seed = 123)
summ_fit3 <- summary(fit3)

fig_pro_primary <- plot_clme(
    summ_fit3, 
    group = c("G1", "G2", "G3", "G4"),
    y_min = 0, y_max = 0.25, 
    p_gap = 0.05, ann_pos = 0.22) +
  scale_fill_npg(name = NULL) +
  labs(x = NULL, y = "Propionate")

fig_pro_primary

在这里插入图片描述

Primary grouping: Valerate

短链脂肪酸Valerate与Primary grouping的相关关系

fit4 <- clme(valerate_v1 ~ group1 + abx_use, data = df_v1, constraints = cons, seed = 123)
summ_fit4 <- summary(fit4)

fig_val_primary <- plot_clme(
    summ_fit4, 
    group = c("G1", "G2", "G3", "G4"),
    y_min = 0, y_max = 0.053, 
    p_gap = 0.009, ann_pos = 0.048) +
  scale_fill_npg(name = NULL) +
  labs(x = NULL, y = "Valerate")

fig_val_primary

在这里插入图片描述

Secondary grouping: Acetate

短链脂肪酸Acetate与Secondary grouping的相关关系

fit1 <- clme(acetate_v1 ~ group2 + abx_use, data = df_v1, constraints = cons, seed = 123)
summ_fit1 <- summary(fit1)

fig_ace_secondary <- plot_clme(summ_fit1, group = c("G1", "G2", "G3", "G4", "G5"), 
                              y_min = 0, y_max = 4, p_gap = 0.7, ann_pos = 3.5) +
  scale_fill_npg(name = NULL) +
  labs(x = NULL, y = "Acetate")

fig_ace_secondary

在这里插入图片描述

Secondary grouping: Butyrate

短链脂肪酸Butyrate与Secondary grouping的相关关系

fit2 <- clme(butyrate_v1 ~ group2 + abx_use, data = df_v1, constraints = cons, seed = 123)
summ_fit2 <- summary(fit2)

fig_but_secondary <- plot_clme(summ_fit2, group = c("G1", "G2", "G3", "G4", "G5"), 
                              y_min = 0, y_max = 0.18, p_gap = 0.04, ann_pos = 0.16) +
  scale_fill_npg(name = NULL) +
  labs(x = NULL, y = "Butyrate")

fig_but_secondary

在这里插入图片描述

Secondary grouping: Propionate

短链脂肪酸Propionate与Secondary grouping的相关关系

fit3 <- clme(propionate_v1 ~ group2 + abx_use, data = df_v1, constraints = cons, seed = 123)
summ_fit3 <- summary(fit3)

fig_pro_secondary <- plot_clme(summ_fit3, group = c("G1", "G2", "G3", "G4", "G5"),
                              y_min = 0, y_max = 0.25, p_gap = 0.05, ann_pos = 0.22) +
  scale_fill_npg(name = NULL) +
  labs(x = NULL, y = "Propionate")

fig_pro_secondary

在这里插入图片描述

Secondary grouping: Valerate

短链脂肪酸Valerate与Secondary grouping的相关关系

fit4 <- clme(valerate_v1 ~ group2 + abx_use, data = df_v1, constraints = cons, seed = 123)
summ_fit4 <- summary(fit4)

fig_val_secondary <- plot_clme(summ_fit4, group = c("G1", "G2", "G3", "G4", "G5"),
                              y_min = 0, y_max = 0.053, p_gap = 0.009, ann_pos = 0.048) +
  scale_fill_npg(name = NULL) +
  labs(x = NULL, y = "Valerate")

fig_val_secondary

在这里插入图片描述

生信学习者2
关注
  • 9
    点赞
  • 踩
  • 25
    收藏
    觉得还不错? 一键收藏
  • 打赏
    打赏
  • 0
    评论
专栏目录
评论
添加红包

请填写红包祝福语或标题

个

红包个数最小为10个

元

红包金额最低5元

当前余额3.43元 前往充值 >
需支付：10.00元
成就一亿技术人!
领取后你会自动成为博主和红包主的粉丝 规则
hope_wisdom
发出的红包

打赏作者

生信学习者2

你的鼓励将是我创作的最大动力

¥1 ¥2 ¥4 ¥6 ¥10 ¥20
扫码支付：¥1
获取中
扫码支付

您的余额不足，请更换扫码支付或充值

打赏作者

实付元
使用余额支付
点击重新获取
扫码支付
钱包余额 0

抵扣说明：

1.余额是钱包充值的虚拟货币，按照1:1的比例进行支付金额的抵扣。
2.余额无法直接购买下载，可以购买VIP、付费专栏及课程。

余额充值