Last updated: 2025-04-07

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Introduction

The Susie st models are trained here https://sq-96.github.io/multigroup_ctwas_analysis/data_weight_training_fusionscale_rsqupdated_allhaveqtl.html

The Munro’s model are from this paper https://www.nature.com/articles/s41467-024-54840-8

library(ctwas)
library(ggplot2)
library(tidyverse)

source("/project/xinhe/xsun/multi_group_ctwas/data/samplesize.R")

folder_results_munroST <- "/project/xinhe/shengqian/ctwas_GWAS_analysis/snakemake_outputs/"
folder_results_susieST <- "/project/xinhe/xsun/multi_group_ctwas/15.susie_weights/snakemake_outputs/"
folder_results_woST <- "/project/xinhe/shengqian/ctwas_GWAS_analysis/snakemake_outputs/"

# mapping_predictdb <- readRDS("/project2/xinhe/shared_data/multigroup_ctwas/weights/mapping_files/PredictDB_mapping.RDS")
# mapping_munro <- readRDS("/project2/xinhe/shared_data/multigroup_ctwas/weights/mapping_files/Munro_mapping.RDS")
# mapping_two <- rbind(mapping_predictdb,mapping_munro)

colors <- c(  "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728",  "#9467bd", "#8c564b", "#e377c2", "#7f7f7f",  "#bcbd22",  "#17becf",  "#f7b6d2",  "#c5b0d5",  "#9edae5", "#ffbb78",  "#98df8a",  "#ff9896" )

plot_piechart <- function(ctwas_parameters, colors, by, title) {
  # Create the initial data frame
  data <- data.frame(
    category = names(ctwas_parameters$prop_heritability),
    percentage = ctwas_parameters$prop_heritability
  )
  
  # Split the category into context and type
  data <- data %>%
    mutate(
      context = sub("\\|.*", "", category),
      type = sub(".*\\|", "", category)
    )
  
  # Aggregate the data based on the 'by' parameter
  if (by == "type") {
    data <- data %>%
      group_by(type) %>%
      summarize(percentage = sum(percentage)) %>%
      mutate(category = type)  # Use type as the new category
  } else if (by == "context") {
    data <- data %>%
      group_by(context) %>%
      summarize(percentage = sum(percentage)) %>%
      mutate(category = context)  # Use context as the new category
  } else {
    stop("Invalid 'by' parameter. Use 'type' or 'context'.")
  }
  
  # Calculate percentage labels for the chart
  data$percentage_label <- paste0(round(data$percentage * 100, 1), "%")
  
  # Create the pie chart
  pie <- ggplot(data, aes(x = "", y = percentage, fill = category)) +
    geom_bar(stat = "identity", width = 1) +
    coord_polar("y", start = 0) +
    theme_void() +  # Remove background and axes
    geom_text(aes(label = percentage_label), 
              position = position_stack(vjust = 0.5), size = 3) +  # Adjust size as needed
    scale_fill_manual(values = colors) +  # Custom colors
    labs(fill = "Category") +  # Legend title
    ggtitle(title)  # Title
  
  return(pie)
}

LDL-ukb-d-30780_irnt

Setting: shared_all, thin = 0.1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_all, thin = 0.5

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_all, thin = 1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 0.1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 0.5

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

IBD-ebi-a-GCST004131

Setting: shared_all, thin = 0.1

trait <- "IBD-ebi-a-GCST004131"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_all, thin = 0.5

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_all, thin = 1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 0.1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 0.5

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

T2D-panukb

Setting: shared_all, thin = 0.1

trait <- "T2D-panukb"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_all, thin = 0.5

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_all, thin = 1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 0.1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 0.5

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

BMI-panukb

Setting: shared_all, thin = 0.1

trait <- "BMI-panukb"
thin <- 0.1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_all, thin = 0.5

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.5
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_all, thin = 1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 1
var_struc <- "shared_all"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 0.1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 0.5

trait <- "LDL-ukb-d-30780_irnt"
thin <- 0.5
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))

Setting: shared_type, thin = 1

trait <- "LDL-ukb-d-30780_irnt"
thin <- 1
var_struc <- "shared_type"

gwas_n <- samplesize[trait]
st <- "without_ST"

param_woST <- readRDS(paste0(folder_results_woST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_woST <- summarize_param(param_woST, gwas_n)
total_nonSNPpve_woST <- 1- ctwas_parameters_woST$prop_heritability["SNP"]
pve_pie_by_type_woST <- plot_piechart(ctwas_parameters = ctwas_parameters_woST, colors = colors, by = "type", title = paste0("withoutST - nonSNP %h2g:",round(total_nonSNPpve_woST, digits = 4)))
st <- "with_susieST"

param_susieST <- readRDS(paste0(folder_results_susieST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))


ctwas_parameters_susieST <- summarize_param(param_susieST, gwas_n)
total_nonSNPpve_susieST <- 1- ctwas_parameters_susieST$prop_heritability["SNP"]
pve_pie_by_type_susieST <- plot_piechart(ctwas_parameters = ctwas_parameters_susieST, colors = colors, by = "type", title = paste0("susieST - nonSNP %h2g:",round(total_nonSNPpve_susieST, digits = 4)))
st <- "with_ST"
param_munroST <- readRDS(paste0(folder_results_munroST,"/",trait,"/",trait,".",st,".thin",thin,".",var_struc,".param.RDS"))

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)

ctwas_parameters_munroST <- summarize_param(param_munroST, gwas_n)
total_nonSNPpve_munroST <- 1- ctwas_parameters_munroST$prop_heritability["SNP"]
pve_pie_by_type_munroST <- plot_piechart(ctwas_parameters = ctwas_parameters_munroST, colors = colors, by = "type", title = paste0("munroST - nonSNP %h2g:",round(total_nonSNPpve_munroST, digits = 4)))
gridExtra::grid.arrange(pve_pie_by_type_woST, pve_pie_by_type_susieST,pve_pie_by_type_munroST, 
                        ncol = 3, top = paste0(trait,"-thin",thin,"-",var_struc))        


sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.1    stringr_1.5.1    dplyr_1.1.4      purrr_1.0.2     
 [5] readr_2.1.2      tidyr_1.3.0      tibble_3.2.1     tidyverse_1.3.1 
 [9] ggplot2_3.5.1    ctwas_0.5.4.9000

loaded via a namespace (and not attached):
  [1] colorspace_2.0-3            rjson_0.2.21               
  [3] ellipsis_0.3.2              rprojroot_2.0.3            
  [5] XVector_0.36.0              locuszoomr_0.2.1           
  [7] GenomicRanges_1.48.0        base64enc_0.1-3            
  [9] fs_1.5.2                    rstudioapi_0.13            
 [11] farver_2.1.0                ggrepel_0.9.1              
 [13] bit64_4.0.5                 lubridate_1.8.0            
 [15] AnnotationDbi_1.58.0        fansi_1.0.3                
 [17] xml2_1.3.3                  codetools_0.2-18           
 [19] logging_0.10-108            cachem_1.0.6               
 [21] knitr_1.39                  jsonlite_1.8.0             
 [23] workflowr_1.7.0             Rsamtools_2.12.0           
 [25] broom_0.8.0                 dbplyr_2.1.1               
 [27] png_0.1-7                   compiler_4.2.0             
 [29] httr_1.4.3                  backports_1.4.1            
 [31] assertthat_0.2.1            Matrix_1.5-3               
 [33] fastmap_1.1.0               lazyeval_0.2.2             
 [35] cli_3.6.1                   later_1.3.0                
 [37] htmltools_0.5.2             prettyunits_1.1.1          
 [39] tools_4.2.0                 gtable_0.3.0               
 [41] glue_1.6.2                  GenomeInfoDbData_1.2.8     
 [43] rappdirs_0.3.3              Rcpp_1.0.12                
 [45] Biobase_2.56.0              cellranger_1.1.0           
 [47] jquerylib_0.1.4             vctrs_0.6.5                
 [49] Biostrings_2.64.0           rtracklayer_1.56.0         
 [51] xfun_0.41                   rvest_1.0.2                
 [53] irlba_2.3.5                 lifecycle_1.0.4            
 [55] restfulr_0.0.14             ensembldb_2.20.2           
 [57] XML_3.99-0.14               zlibbioc_1.42.0            
 [59] zoo_1.8-10                  scales_1.3.0               
 [61] gggrid_0.2-0                hms_1.1.1                  
 [63] promises_1.2.0.1            MatrixGenerics_1.8.0       
 [65] ProtGenerics_1.28.0         parallel_4.2.0             
 [67] SummarizedExperiment_1.26.1 AnnotationFilter_1.20.0    
 [69] LDlinkR_1.2.3               yaml_2.3.5                 
 [71] curl_4.3.2                  gridExtra_2.3              
 [73] memoise_2.0.1               sass_0.4.1                 
 [75] biomaRt_2.54.1              stringi_1.7.6              
 [77] RSQLite_2.3.1               highr_0.9                  
 [79] S4Vectors_0.34.0            BiocIO_1.6.0               
 [81] GenomicFeatures_1.48.3      BiocGenerics_0.42.0        
 [83] filelock_1.0.2              BiocParallel_1.30.3        
 [85] repr_1.1.4                  GenomeInfoDb_1.39.9        
 [87] rlang_1.1.2                 pkgconfig_2.0.3            
 [89] matrixStats_0.62.0          bitops_1.0-7               
 [91] evaluate_0.15               lattice_0.20-45            
 [93] labeling_0.4.2              GenomicAlignments_1.32.0   
 [95] htmlwidgets_1.5.4           cowplot_1.1.1              
 [97] bit_4.0.4                   tidyselect_1.2.0           
 [99] magrittr_2.0.3              AMR_2.1.1                  
[101] R6_2.5.1                    IRanges_2.30.0             
[103] generics_0.1.2              DelayedArray_0.22.0        
[105] DBI_1.2.2                   haven_2.5.0                
[107] withr_2.5.0                 pgenlibr_0.3.3             
[109] pillar_1.9.0                KEGGREST_1.36.3            
[111] RCurl_1.98-1.7              mixsqp_0.3-43              
[113] modelr_0.1.8                crayon_1.5.1               
[115] utf8_1.2.2                  BiocFileCache_2.4.0        
[117] plotly_4.10.0               tzdb_0.4.0                 
[119] rmarkdown_2.25              progress_1.2.2             
[121] readxl_1.4.0                grid_4.2.0                 
[123] data.table_1.14.2           blob_1.2.3                 
[125] git2r_0.30.1                reprex_2.0.1               
[127] digest_0.6.29               httpuv_1.6.5               
[129] stats4_4.2.0                munsell_0.5.0              
[131] viridisLite_0.4.0           skimr_2.1.4                
[133] bslib_0.3.1