Make gene track plot using Gviz

track_plot(
  finemapstats,
  region,
  gene.annots,
  bigSNP = NULL,
  txdb = NULL,
  counts = NULL,
  peaks = NULL,
  loops = NULL,
  genome = "hg19",
  filter_loop_genes = NULL,
  filter_loop_snps = NULL,
  filter_protein_coding_genes = TRUE,
  color_piptrack_by = c("locus", "cs", "none"),
  highlight_snps = NULL,
  counts.ylim = c(0, 1),
  counts.color,
  peaks.color = "navy",
  loops.color = "gray",
  highlight.color = "pink",
  genelabel.side = c("above", "below", "left", "right"),
  track.sizes = NULL,
  rotation.title = 0,
  verbose = FALSE,
  ...
)

Arguments

finemapstats: A GRanges object of processed finemapping summary statistics
region: The genomic region to visualize in the format of "chr:start-end".
gene.annots: A GRanges object of gene annotations
bigSNP: A bigsnpr object attached via bigsnpr::snp_attach()
txdb: A txdb object of gene annotations
counts: A list of counts data to display as quantitativ data tracks
peaks: A list of peaks to display as binary data tracks
loops: A list of chromatin loops, e.g. PC-HiC, ABC, etc.
genome: Genome assembly version (default: "hg19").
filter_loop_genes: A vector of gene names. Only show loops connected to the genes.
filter_loop_snps: A vector of SNP IDs. Only show loops connected to the SNPs.
filter_protein_coding_genes: Logical. If TRUE, only shows protein coding gene.
color_piptrack_by: Color SNPs in the PIP track by locus, cs (credible sets), or none (same color).
highlight_snps: SNPs (rsIDs) to highlight. Or highlight top SNP ('topSNP').
counts.ylim: ylim range (default: between 0 and 1) for the counts tracks
counts.color: Colors for the counts tracks
peaks.color: Colors for the peak tracks
highlight.color: Colors for the highlighted SNPs
genelabel.side: Side to put gene labels, options are: 'above' (default), 'below', 'left', 'right'.
track.sizes: Sizes of the tracks
rotation.title: The rotation angle for the text in the track title
verbose: If TRUE, print detail messages for plotting