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