孟德尔随机化简单复现（1）-精神疾病和骨质疏松的相关性

参考文献：Mendelian randomization analysis does not reveal a causal influence of mental diseases on osteoporosis（孟德尔随机化分析未揭示精神疾病对骨质疏松症的因果影响）

文章框架：

 （1）绘制总的森林图

#制定函数批量处理数据
datamr<-function(x){
  library(magrittr)
  out<-combined_table[combined_table$method==x,] %>% generate_odds_ratios()
  fenge<-function(x){
    split_string <- strsplit(x, "||", fixed = TRUE)
    result <- split_string[[1]][1]
    return(result)
    }
  out_1<-out
  out_1[,3:4]<-apply(out_1[,3:4],2,function(x) sapply(x, fenge))
  #重新排列
  #指定排序顺序
  out_1$outcome
  order_vec <- c("Forearm bone mineral density ", "Lumbar spine bone mineral density ", "Femoral neck bone mineral density ",
               "Total body bone mineral density ")
  #根据指定顺序排序数据框
  out_2 <- out_1[order(match(out_1$outcome, order_vec)), ]
  #修改数据适合绘制森林图
  out_2$outcome[-seq(3, nrow(out_2), by = 5)] <-""
  out_2$`OR(95%CI)`<-sprintf("%.2f(%.2f to %.2f)",out_2$or,out_2$or_lci95,out_2$or_uci95)
  return(out_2)
}
#IVW
IVW<-datamr("Inverse variance weighted")
#IVW(fixed-effect)
`IVW(fixed-effect)`<-datamr("Inverse variance weighted (fixed effects)")
#绘制多组的森林图
new_colnames <- paste0(colnames(`IVW(fixed-effect)`), "_2")
colnames(`IVW(fixed-effect)`) <- new_colnames
dt<-cbind(IVW,`IVW(fixed-effect)`)
dt$` `<-paste(rep(" ", dim(dt)[1]), collapse = " ")
dt$`  `<-paste(rep(" ", dim(dt)[1]), collapse = " ")
colnames(dt)
#绘制基本图形
tm <- forest_theme(base_size = 8, # 文字大小
                   #可信区间
                   ci_pch = 10,#点形状
                   ci_col = "red", #颜色
                   ci_lty = 1,#线条类型
                   ci_lwd = 4,#线宽度
                   ci_Theight = 0.2, #两端加短竖线
                   # 参考线
                   refline_lwd = 1,#宽度
                   refline_lty = "dashed",#类型
                   refline_col = "black",#颜色
                   # 汇总菱形
                   summary_fill = "blue",#填充色
                   summary_col = "blue",#边框色
                   # 脚注
                   footnote_cex = 0.6,#大小
                   footnote_fontface = "italic",#字体
                   footnote_col = "black")#颜色
p <-forest(dt[,c(3,4,31,15,18,19,32,30)],
           est = list(dt$or,
                      dt$or_2),
           lower = list(dt$or_lci95,
                        dt$or_lci95_2),
           upper = list(dt$or_uci95,
                        dt$or_uci95_2),
           ci_column = c(3, 7),
           ref_line = 1,
           xlim = c(0.01,100),x_trans ="log10",
           ticks_at = c(0.01,0.1,1,10,100),
           #vert_line = c(1,2),
           #nudge_y = 0.2,
           theme = tm)
p
#顶部插入信息
p1<-insert_text(p,text =c("IVW","IVW(fixed-effect)"),
                col = c(2,6),
                part = "header",
                gp = gpar(fontface =
                           "bold"))
p1
#在标题下方加一条下划线
p2 <-add_border(p1, 
                row =c(1),
                col=c(1:3,5:7),
                part = "header")
p2
#为标题的两行添加下划线
p3 <-add_border(p2, 
                row =c(0,2),
                col=1:8,
                part = "header")
p3

（2）绘制留一法森林图

Mydata<- harmonise_data(exposure_dat=wer,
                        outcome_dat=asd,
                        action= 2)
leave<- mr_leaveoneout(Mydata)
mr_leaveoneout_plot(leave)

 3、散点图、森林图、漏斗图

#定义了5种方法，包括固定效应和随机效应模型
random<-mr(Mydata,method_list=c("mr_ivw", "mr_ivw_fe",
                             "mr_two_sample_ml",
                             "mr_egger_regression", "mr_weighted_median",
                             "mr_penalised_weighted_median",
                             "mr_simple_mode", "mr_weighted_mode"))
#散点图
mr_scatter_plot(random,Mydata)
#森林图
forest<- mr_singlesnp(Mydata)
mr_forest_plot(forest)
#漏斗图
mr_funnel_plot(forest)
#生成OR和可信区间
out<-generate_odds_ratios(random)