gg_Manhattan_Zoom
gg_Manhattan_Zoom.RdUsage
gg_Manhattan_Zoom(
folder = "GWAS_Results/",
trait = list_Traits(folder)[1],
title = trait,
chr = 1,
pos1 = NULL,
pos2 = NULL,
addGenome = T,
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,
facet = F,
pmax = NULL,
models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM", "CMLM", "SUPER"),
model.colors = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkorchid4",
"blue2", "magenta3"),
sig.color = "black",
legend.rows = 1,
legend.box = "horizontal",
point.sizes = c(0.3, 1, 0.75),
plotHBPvalues = F,
skyline = NULL
)Arguments
- folder
Folder containing GWAS results.
- trait
The trait to read.
- title
A title for the plot.
- chr
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.
- facet
Logical, whether or not to produce a facetted or multi-model plot. Default is
facet = F.- pmax
A max value for the y-axis.
- models
Models to read.
- model.colors
Colors for each model. Used if
facet = F.- sig.color
Color for significant assoctiations.
- legend.rows
Number of rows for the legend.
- legend.box
Alignment of the legend. Default is "horizontal", but it can be changed to "vertical".
- point.sizes
Sizes for the points. c("Not Sig", "Sig", "Sug").
- 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.