track_plot: Make gene track plot using Gviz

In kevinlkx/Mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Make gene track plot using Gviz

Description

Make gene track plot using Gviz

Usage

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

kevinlkx/Mapgen documentation built on April 2, 2024, 5:48 a.m.