Plots the cTWAS result for a single locus

Usage

make_locusplot(
  finemap_res,
  region_id,
  ens_db,
  weights = NULL,
  R_snp_gene = NULL,
  R_gene = NULL,
  locus_range = NULL,
  focal_id = NULL,
  focal_gene = NULL,
  filter_protein_coding_genes = TRUE,
  filter_cs = TRUE,
  color_pval_by = c("cs", "LD", "none"),
  color_pip_by = c("cs", "LD", "none"),
  LD.breaks = c(0, 0.2, 0.4, 0.6, 0.8, 1),
  LD.colors = c("grey", "cyan", "green", "orange", "red", "salmon"),
  L = 5,
  cs.colors = c("firebrick", "dodgerblue", "forestgreen", "darkmagenta", "darkorange",
    "grey"),
  focal.colors = c("grey", "salmon"),
  label_QTLs = TRUE,
  highlight_pval = NULL,
  highlight_pip = 0.8,
  highlight_pos = NULL,
  highlight.color = "red",
  highlight.pos.color = "magenta",
  point.sizes = c(1, 3),
  point.alpha = c(0.4, 0.6),
  point.shapes = c(16, 15, 18, 17, 10, 12, 14, 11),
  label.text.size = 2.5,
  max.overlaps = 10,
  axis.text.size = 8,
  axis.title.size = 10,
  legend.text.size = 9,
  legend.position = "top",
  legend.nrow = c(1, 1),
  genelabel.cex.text = 0.7,
  panel.heights = c(4, 4, 1, 4),
  verbose = FALSE
)

Arguments

finemap_res: a data frame of cTWAS finemapping result
region_id: region ID to be plotted
ens_db: Ensembl database
weights: a list of proprocessed weights, used to plot QTL track. If NULL, will not plot the QTL track.
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_id: the focal ID.
focal_gene: the focal gene name. By default, use the gene with the highest PIP.
filter_protein_coding_genes: If TRUE, limits to protein coding genes only.
filter_cs: If TRUE, limits to credible sets.
color_pval_by: Options to color the p-value track. "LD": colors the p-value track by the correlations to the focal gene. "cs": colors the p-value track by the credible sets. "none": uses the same color for non-focal genes.
color_pip_by: Options to color the PIP track. "LD": colors the PIP track by the correlations to the focal gene. "cs": colors the PIP track by the credible sets. "none": uses the same color for non-focal genes.
LD.breaks: Breaks of LD intervals.
LD.colors: Colors for correlation levels.
L: Number of effects in finemapping.
cs.colors: Colors for credible sets.
focal.colors: Colors for non-focal and focal gene.
label_QTLs: If TRUE, label SNP IDs in the QTL panel.
highlight_pval: p-value to highlight with a horizontal line
highlight_pip: PIP to highlight with a horizontal line
highlight_pos: genomic positions to highlight with vertical lines
highlight.color: color for horizontal lines highlighting p-values and PIPs.
highlight.pos.color: color for vertical lines highlighting genomic positions.
point.sizes: size values for SNP and non-SNP data points in the scatter plots
point.alpha: alpha values for SNP and non-SNP 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
max.overlaps: Setting for geom_text_repel() function to label texts. Exclude text labels when they overlap too many other things.
axis.text.size: Font size for axis label text.
axis.title.size: Font size for axis title text.
legend.text.size: Font size for legend text.
legend.position: position to put legends. If "none", no legends will be shown.
legend.nrow: Number of rows for legend text in the panels.
genelabel.cex.text: Controls the size of the gene labels.
panel.heights: Relative heights of the panels.
verbose: If TRUE, print detail messages.