gg_Manhattan_Zoom
gg_Manhattan_Zoom.RdCreates a manhattan plot zoomed in to a particular region.
Usage
gg_Manhattan_Zoom(
folder = "GWAS_Results/",
trait = list_Traits(folder)[1],
title = trait,
chrom,
pos1,
pos2,
threshold = NULL,
sug.threshold = NULL,
markers = NULL,
labels = markers,
vlines = markers,
vline.colors = rep("red", length(vlines)),
vline.types = rep(1, length(vlines)),
vline.legend = T,
pmax = NULL,
models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM", "CMLM", "SUPER"),
model.colors = gwaspr_Colors,
facet = F,
highlight.sig = F,
sig.color = "red",
legend.rows = 1,
plotHBPvalues = F,
skyline = "Kansas"
)Arguments
- folder
Folder containing GWAS results.
- trait
The trait to read.
- title
A title for the plot.
- chrom
Chromosome to plot.
- pos1
Start position on chromosome.
- pos2
End position on chromosome.
- threshold
Significant Threshold.
- sug.threshold
Suggested threshold.
- markers
Markers to be labelled.
- labels
Labels to be used for markers.
- 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.
- pmax
A max value for the y-axis.
- models
Models to read.
- model.colors
Colors for each model. Used if `facet = F`.
- facet
Logical, whether or not to produce a facetted or multi-model plot. Default is `facet = F`.
- highlight.sig
Logical, whether or not to highlight significant associations with a black circle. Used if `facet = F`.
- sig.color
Color for significant assoctiations.
- legend.rows
Number of rows for the legend.
- plotHBPvalues
Logical, should H.B.P.Values be uses.
- skyline
Which skyline type to use. Can be "NYC" or "Kansas". If left NULL, it will use the highest P.value.
- addQQ
Logical, whether or not to add a QQ plot
- 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").