snp_track_merged: SNP track merged

In bschilder/echoplot: echoverse module: Locus plot creation for fine-mapping and colocalization studies

SNP track merged

Description

Manhattan plot of GWAS/QTL data with various fine-mapping related annotations. Support function for plot_locus.

Usage

snp_track_merged(
  dat,
  yvar = "-log10(P)",
  labels_subset = c("Lead", "CS", "UCS", "Consensus"),
  absolute_labels = FALSE,
  label_type = "rsid_only",
  label_leadsnp = TRUE,
  sig_cutoff = 5e-08,
  point_alpha = 0.5,
  show.legend = TRUE,
  xtext = TRUE,
  facet_formula = "Method~.",
  dataset_type = NULL,
  genomic_units = "POS",
  remove_duplicates = FALSE,
  strip.text.y.angle = 0,
  show_plot = FALSE,
  verbose = TRUE
)

Arguments

dat	Data to query transcripts with.
labels_subset	Include colored shapes and RSID labels to help highlight SNPs belonging to one or more of the following groups: Lead, Credible Set, Consensus.
sig_cutoff	Filters out SNPs to plot based on an (uncorrected) p-value significance cutoff.
point_alpha	Opacity of each data point.
xtext	Include x-axis title and text for each track (not just the lower-most one).
facet_formula	Formula to facet plots by. See facet_grid for details.
dataset_type	Dataset type (e.g. "GWAS" or "eQTL").
genomic_units	Which genomic units to return window limits in.
remove_duplicates	Remove duplicate labels when SNPs are part of >1 group in labels_subset.
strip.text.y.angle	Angle of the y-axis facet labels.
show_plot	Print plot to screen.
verbose	Print messages.

Examples

dat <- echodata::BST1[seq_len(100),]
plt <- snp_track_merged(dat = dat, yvar="PP", show_plot=TRUE)

bschilder/echoplot documentation built on Oct. 26, 2023, 6:55 p.m.