Last updated: 2025-06-06

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File	Version	Author	Date	Message
Rmd	cb09c9c	XSun	2025-06-06	update
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html	4fc641c	XSun	2025-06-05	update

Introduction

library(ggplot2)
library(gridExtra)

trait_nopsy <- c("LDL-ukb-d-30780_irnt","IBD-ebi-a-GCST004131","aFib-ebi-a-GCST006414","SBP-ukb-a-360",
                 "T1D-GCST90014023","T2D-panukb","ATH_gtexukb","BMI-panukb","HB-panukb",
                 "Height-panukb","HTN-panukb","PLT-panukb","RA-panukb","RBC-panukb",
                 "WBC-ieu-b-30"
                 )
trait_psy <- c("SCZ-ieu-b-5102","ASD-ieu-a-1185","BIP-ieu-b-5110","MDD-ieu-b-102","PD-ieu-b-7",
               "ADHD-ieu-a-1183","NS-ukb-a-230")
traits <- c(trait_nopsy,trait_psy)

folder_results_multi <- "/project/xinhe/xsun/multi_group_ctwas/23.multi_group_0515/snakemake_outputs/"


load_finemap_gene_data <- function(filepath) {
  if (file.exists(filepath)) {
    data <- readRDS(filepath)$finemap_res
    return(data[data$type != "SNP", ])
  }
  return(NULL)
}

plot_finemap_data <- function(data, trait, problematic_genes = NULL, alpha = 0.4, title_suffix = NULL) {
  if (!is.null(title_suffix)) {
    plot_title <- paste0(title_suffix, " - ", trait)
  } else {
    plot_title <- trait
  }
  
  if (!is.null(problematic_genes)) {
    data$problematic <- data$id %in% problematic_genes
    ggplot(data, aes(x = abs(z), y = susie_pip, color = problematic)) +
      geom_point(alpha = alpha) +
      labs(
        x = "Absolute Z-score",
        y = "SuSiE PIP",
        title = plot_title,
        color = "Problematic"
      ) +
      scale_color_manual(values = c("FALSE" = "black", "TRUE" = "red")) +
      theme_minimal()
  } else {
    ggplot(data, aes(x = abs(z), y = susie_pip)) +
      geom_point(alpha = alpha, color = "black") +
      labs(
        x = "Absolute Z-score",
        y = "SuSiE PIP",
        title = plot_title
      ) +
      theme_minimal()
  }
}

Diagnosis plots

for (trait in traits){
  
  rm(p_origin,p_regionmerge,p_ldmismatch)
  
  # Load origin data (always expected)
  file_origin <- paste0(folder_results_multi, trait, "/", trait, ".3qtls.thin1.shared_all.L5.finemap_regions_res.RDS")
  finemap_res_gene_origin <- load_finemap_gene_data(file_origin)
  
  # Load problematic gene list (optional)
  file_problematic_genes <- paste0(folder_results_multi, trait, "/", trait, ".3qtls.thin1.shared_all.L5.ldmismatch_problematic_genes.RDS")
  problematic_genes <- if (file.exists(file_problematic_genes)) readRDS(file_problematic_genes) else NULL
  
  p_origin <- plot_finemap_data(finemap_res_gene_origin, trait, problematic_genes, title_suffix = "origin")
  
  # Plot regionmerge if file exists
  file_regionmerge <- paste0(folder_results_multi,trait,"/",trait,".3qtls.thin1.shared_all.L5.regionmerge_finemap_regions_res.RDS")
  if (file.exists(file_regionmerge)) {
    finemap_res_gene_regionmerge <- load_finemap_gene_data(file_regionmerge)
    p_regionmerge <- plot_finemap_data(finemap_res_gene_regionmerge, trait, problematic_genes, title_suffix = "regionmerge")
  }
  
  # Plot ldmismatch if file exists
  file_ldmismatch <- paste0(folder_results_multi,trait,"/",trait,".3qtls.thin1.shared_all.L5.ldmismatch_noLD_finemap_regions_res.RDS")
  if (file.exists(file_ldmismatch)) {
    finemap_res_gene_ldmismatch <- load_finemap_gene_data(file_ldmismatch)
    p_ldmismatch <- plot_finemap_data(finemap_res_gene_ldmismatch, trait, problematic_genes, title_suffix = "ldmismatch")
  }
  
  
  # Collect existing plots
  plot_list <- list()
  
  if (exists("p_origin")) plot_list <- c(plot_list, list(p_origin))
  if (exists("p_regionmerge")) plot_list <- c(plot_list, list(p_regionmerge))
  if (exists("p_ldmismatch")) plot_list <- c(plot_list, list(p_ldmismatch))
  
  # Only call grid.arrange if at least one plot exists
  if (length(plot_list) > 0) {
    do.call(grid.arrange, c(plot_list, nrow = 1))
  }
  
  
}

Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_origin' not
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Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_regionmerge' not
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Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_ldmismatch' not
found

Version	Author	Date
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Version	Author	Date
4fc641c	XSun	2025-06-05

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Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_ldmismatch' not
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Version	Author	Date
4fc641c	XSun	2025-06-05

Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_regionmerge' not
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Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_ldmismatch' not
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4fc641c	XSun	2025-06-05

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Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_ldmismatch' not
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Version	Author	Date
4fc641c	XSun	2025-06-05

Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_regionmerge' not
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Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_ldmismatch' not
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Version	Author	Date
4fc641c	XSun	2025-06-05

Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_regionmerge' not
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Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_ldmismatch' not
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Version	Author	Date
4fc641c	XSun	2025-06-05

Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_regionmerge' not
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Warning in rm(p_origin, p_regionmerge, p_ldmismatch): object 'p_ldmismatch' not
found

Version	Author	Date
4fc641c	XSun	2025-06-05

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4fc641c	XSun	2025-06-05

Examples

IBD-ebi-a-GCST004131

WBC-ieu-b-30

region 1_22760390_23594100

region 1_25190354_27075376

region 3_140235755_141620255

region 12_12580594_15088550

HB-panukb

region 1_3666172_4320751

region 14_63323296_64753580

Height-panukb

region 6_109983044_112023811

region 22_40149793_42294812

region 17_29007226_31459473

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] gridExtra_2.3 ggplot2_3.5.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.12      highr_0.9        pillar_1.9.0     compiler_4.2.0  
 [5] bslib_0.3.1      later_1.3.0      jquerylib_0.1.4  git2r_0.30.1    
 [9] workflowr_1.7.0  tools_4.2.0      digest_0.6.29    jsonlite_1.8.0  
[13] evaluate_0.15    lifecycle_1.0.4  tibble_3.2.1     gtable_0.3.0    
[17] pkgconfig_2.0.3  rlang_1.1.2      cli_3.6.1        rstudioapi_0.13 
[21] yaml_2.3.5       xfun_0.41        fastmap_1.1.0    withr_2.5.0     
[25] dplyr_1.1.4      stringr_1.5.1    knitr_1.39       generics_0.1.2  
[29] fs_1.5.2         vctrs_0.6.5      sass_0.4.1       tidyselect_1.2.0
[33] rprojroot_2.0.3  grid_4.2.0       glue_1.6.2       R6_2.5.1        
[37] fansi_1.0.3      rmarkdown_2.25   farver_2.1.0     magrittr_2.0.3  
[41] whisker_0.4      scales_1.3.0     promises_1.2.0.1 htmltools_0.5.2 
[45] colorspace_2.0-3 httpuv_1.6.5     labeling_0.4.2   utf8_1.2.2      
[49] stringi_1.7.6    munsell_0.5.0

Examining the results from multi-group analysis

XSun

2025-06-05