Plots the cTWAS result for a single locus

make_locusplot(
  finemap_res,
  region_id,
  weights,
  ens_db,
  R_snp_gene = NULL,
  R_gene = NULL,
  locus_range = NULL,
  focal_gene = NULL,
  filter_genetrack_biotype = "protein_coding",
  highlight_pval = NULL,
  highlight_pip = 0.8,
  highlight_pos = NULL,
  label_QTLs = TRUE,
  point.sizes = c(1.5, 3.5),
  point.alpha = c(0.4, 0.7),
  point.shapes = c(16, 15),
  label.text.size = 2.5,
  legend.text.size = 10,
  legend.position = "top",
  panel.heights = c(4, 4, 1, 4)
)

Arguments

finemap_res: a data frame of cTWAS finemapping result
region_id: region ID to be plotted
weights: a list of weights
ens_db: Ensembl database
R_snp_gene: SNP-gene correlation matrix of the region. If both R_snp_gene and R_gene are available, color data points with correlations with the focal gene.
R_gene: gene-gene correlation matrix of the region
locus_range: a vector of start and end positions to define the region boundary to be plotted. If NULL, the entire region will be plotted (with 100 bp flanks on both sides).
focal_gene: the focal gene name. If NULL, choose the gene with the highest PIP.
filter_genetrack_biotype: biotype to be displayed in gene tracks. By default, limits to protein coding genes. If NULL, display all possible ones.
highlight_pval: pvalue to highlight with a horizontal line
highlight_pip: PIP to highlight with a horizontal line
highlight_pos: genomic positions to highlight with vertical lines
label_QTLs: If TRUE, label SNP IDs in the QTL panel.
point.sizes: size values for SNP and gene data points in the scatter plots
point.alpha: alpha values for SNP and gene data points in the scatter plots
point.shapes: shapes values for data points of different types in the scatter plots
label.text.size: Font size for gene and SNP label text
legend.text.size: Font size for legend text
legend.position: position to put legends. If "none", no legends will be shown.
panel.heights: Relative heights of the panels.