Make a plot that lines up manhattan and gene locations

Usage

plot_panvar(
  panvar.table.list = NULL,
  gwas.res = NULL,
  ld.list = NULL,
  annotation.table = NULL,
  pvals.in.log = T,
  plot.r2.thresh = 0.2,
  unplotted.alpha = 0.4,
  window,
  sig.line,
  orient = "H",
  qualitative.annotation = NULL,
  qualitative.shape.scale = NULL,
  quantitative.annotation = NULL,
  quantitative.fill.scale = NULL,
  plot.title = "",
  include.gene.id = F,
  highlight.gene.ids = NULL,
  gene.highlight.color = "red",
  annotation.point.variable = "LD",
  annotation.point.scale = NULL,
  plot.effect = F
)

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
annotation.table: table with annotations with columns (geneID, CHR, start, end, annotation). start and end correspond to base-pair coordinates of start and end of gene. CHR is chromosome of gene.
pvals.in.log: boolean, if TRUE PVAL column has already been converted to -log10(pvalue)
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, total window size in KB, all variants within .5 * window are calculated.
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.
plot.title: character, a title for the plot
include.gene.id: boolean, if TRUE, geneID column will be included in annotation plot.
highlight.gene.ids: character, vector of geneID's that will be highlighted in the plot.
gene.highlight.color: character, a color to highlight specific geneIDs
annotation.point.variable: character, variable in annotation.table that indicates how to color points plotted next to gene descriptions. If not supplied, no points are plotted. The input "LD" is reserved and will use LD.
annotation.point.scale: ggplot2 scale object, a color scale to customize how point.color is displayed.
plot.effect: boolean, if TRUE include volcano style effect vs pvalue plot as inset.

Value

ggplot2 object of plot with manhattan plot alongside genes for a given genomic window.

Examples

# work in progress