gg_Manhattan
gg_Manhattan.Rd
Creates a manhattan plot.
Usage
gg_Manhattan(
folder = "GWAS_Results/",
trait = list_Traits(folder)[1],
title = trait,
threshold = NULL,
sug.threshold = NULL,
chrom = NULL,
vlines = markers,
vline.colors = rep("red", length(vlines)),
vline.types = rep(1, length(vlines)),
vline.legend = T,
markers = NULL,
labels = markers,
facet = F,
addQQ = T,
pmax = NULL,
models = c("MLM", "FarmCPU", "BLINK", "MLMM", "GLM", "CMLM", "SUPER"),
model.colors = c("darkgreen", "darkorange3", "steelblue", "darkred", "darkorchid4",
"burlywood4", "darkseagreen4"),
chrom.colors = rep(c("darkgreen", "darkgoldenrod3"), 30),
chrom.unit = "100 Mbp",
legend.rows = 1
)
Arguments
- folder
Folder containing GWAS results.
- trait
The trait to read.
- title
A title for the plot.
- threshold
Significant Threshold.
- sug.threshold
Suggested threshold.
- chrom
Chromosomes to plot. Use if you want to plot a single chromosome.
- vlines
Markers which will be used as a location for a vertical lines.
- vline.colors
colors for each vertical line.
- vline.types
lty for each vertical line.
- vline.legend
Logical, whether or not to add a legend for the vlines.
- markers
Markers to be labelled.
- labels
Labels to be used for markers.
- facet
Logical, whether or not to produce a facetted or multi-model plot.
- addQQ
Logical, whether or not to add a QQ plot
- pmax
A max value for the y-axis.
- models
Models to read.
- model.colors
Colors for each model. Used if `facet = F`.
- chrom.colors
Colors for each chromosome. Used if `facet = T`.
- chrom.unit
Unit for the x-axis. Can be one of c("kbp","100 kbp","Mbp","100 Mbp","Gbp").
- legend.rows
Number of rows for the legend.
- pos1
starting position to plot.
- pos2
ending position to plot.