Make sideways manhattan plot for building locus zoom. Receives output from a single gwas model.

Usage

plot_panvar_manhattan(
  panvar.table.list = NULL,
  gwas.res = NULL,
  ld.list = NULL,
  pvals.in.log = TRUE,
  plot.r2.thresh = 0.2,
  unplotted.alpha = 0.4,
  window,
  sig.line,
  orient = c("H", "V"),
  qualitative.annotation = NULL,
  qualitative.shape.scale = NULL,
  quantitative.annotation = NULL,
  quantitative.fill.scale = NULL
)

Arguments

panvar.table.list: list, output from make_panvar_tables. Provide either this list or both gwas.res and ld.list.
gwas.res: data.frame of all gwas results, should contain columns (CHR, POS, PVAL), corresponding to (chromosome, physical position, and pvalue).
ld.list: list, output of get_ld_in_window
pvals.in.log: boolean, are pvalues in input data.frames in -log10(p)?
plot.r2.thresh: minimum LD with qtl snps to plot snps colored by LD
unplotted.alpha: numeric, number from 0 to 1 to indicate alpha values of snps below the plot.r2.thresh. To not plot these snps set value to 0.
window: numeric, kilobases on either side of top QTL snp to plot
sig.line: numeric, -log10(p) value to draw line on plot
orient: character, will rotate plot 90 degrees. vertical (V) or horizontal (H) refers to how the "buildings" of the plot are plotted. "V" places pvalue on y-axis, "H" places pvalues on x-axis.
qualitative.annotation: character, column in gwas.res that contains qualitative annotations. For example impact grades from snpeff. See format_snpeff_annotations. Will be plotted as shapes. Only accepts up to 5 classes. "IMPACT" and "IMPACT_PLUS" are special cases that will have a pre-assigned scale used if supplied here.
qualitative.shape.scale: ggplot scale, an object with a stored call to ggplot2::scale_shape_manual. More often an output of the function make_consistent_scale.
quantitative.annotation: character, column in gwas.res that contains quantitative annotations. For example, variant effect scores. Will be plotted as fill to points.
quantitative.fill.scale: character or scale object, either a character indicating the option parameter passed to ggplot2::scale_fill_viridis_b that alters the color scale used. Or a previous call to a ggplot2 fill scale for example ggplot2::scale_fill_stepsn.

Value

GGplot of manhattan plot with points colored by R2. Accepts input

Examples

# organize options
tag.snp <- "Chr_05-6857045"
gwas.df <- read.csv(system.file(
    "extdata",
    "PanvarExample_GLM_GWASresults.csv",
    package = "panvaR"))
annotation.table <- read.csv(system.file(
    "extdata",
    "Setaria_shattering_annotation.csv",
    package = "panvaR"))
plink.path <- bigsnpr::download_plink2()
temp.dir <- file.path(tempdir(), "panvar_ex")
dir.create(temp.dir, showWarnings = FALSE)
geno.bed.filename <- "Setaria_shattering_example_pruned.bed"
geno.bed.directory <- system.file("extdata", package="panvaR")

# make input tables
tables <- make_panvar_tables(
  gwas.res = gwas.df,
  tag.snp = tag.snp,
  annotation.table = annotation.table,
  plink.path = plink.path,
  pvals.in.log = F,
  geno.bed.filename = geno.bed.filename,
  geno.bed.directory = geno.bed.directory,
  window = 25,
  temp.dir = temp.dir,
  compute.scores = FALSE,
  snp.to.gene.buffer = 0)
#> Calculating LD
#> Generating snp to gene correspondence
  
# make plot
plot_panvar_manhattan(
  panvar.table.list = tables,
  pvals.in.log = FALSE,
  window = 25,
  sig.line = 6)


# flip it vertical if you want
plot_panvar_manhattan(
  panvar.table.list = tables,
  pvals.in.log = FALSE,
  window = 25,
  sig.line = 6,
  orient = "V")


# clean up
unlink(temp.dir, recursive = TRUE)