gg_Manhattan_xModels
gg_Manhattan_xModels.RdUsage
gg_Manhattan_xModels(
folder = "GWAS_Results/",
traits = list_Traits(folder)[1:2],
title = NULL,
threshold = NULL,
sug.threshold = NULL,
chr = NULL,
markers = NULL,
labels = markers,
vlines = markers,
vline.colors = rep("red", length(vlines)),
vline.types = rep(1, length(vlines)),
legend = F,
legend.rows = 1,
legend.box = "horizontal",
point.sizes = c(0.3, 1, 0.75),
addQQ = T,
pmax = NULL,
pmin = 0,
models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM", "CMLM", "SUPER"),
trait.colors = c("chartreuse4", "firebrick", "steelblue3", "maroon3", "purple3",
"darkgoldenrod4", "tomato3", "aquamarine4", "deeppink3"),
chr.unit = "100 Mbp",
plotHBPvalues = F,
skyline = NULL
)Arguments
- folder
Folder containing GWAS results.
- traits
The traits to read.
- title
A title for the plot.
- threshold
Significant Threshold.
- sug.threshold
Suggested threshold.
- chr
Chromosomes to plot. Use if you want to plot a single chromosome.
- 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.
- legend
Logical, whether or not to add a legend.
- 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").
- addQQ
Logical, whether or not to add a QQ plot.
- pmax
A max value for the y-axis.
- pmin
A min Value for plotting. Markers with lower values will be removed.
- models
Model to read.
- trait.colors
Colors for each trait.
- chr.unit
Unit for the x-axis. Can be one of c("kbp","100 kbp","Mbp","100 Mbp","Gbp").
- skyline
Which skyline type to use. Can be "NYC" or "Kansas". If left NULL, it will use the highest P.value.