Plotting functions for the coloc package
You can plot objects of class coloc, colocBayes and colocABF
Plot results of a coloc.abf run
plot(x, y, ...) ## S4 method for signature 'colocTWAS,missing' plot(x) ## S4 method for signature 'coloc,missing' plot(x, y, ...) ## S4 method for signature 'colocABF,missing' plot(x, y, ...) ## S4 method for signature 'coloc,missing' plot(x, y, ...) ## S4 method for signature 'colocPCs,missing' plot(x) abf.plot(coloc.obj, Pos = 1:nrow(coloc.obj@results), chr = NULL, pos.start = min(Pos), pos.end = max(Pos), trait1 = "trait 1", trait2 = "trait 2")
x |
object to be plotted |
y |
ignored |
... |
other arguments |
coloc.obj |
object of class |
Pos |
positions of all snps in ds1 or in ds2 |
chr |
Chromosome |
pos.start |
lower bound of positions |
pos.end |
upper bound of positions |
trait1 |
name of trait 1 |
trait2 |
name of trait 2 |
If coloc.obj is missing, it will be created as coloc.obj=coloc.abf(ds1,ds2). Both ds1 and ds2 should contain the same snps in the same order
no return value
a ggplot object
Hui Guo, Chris Wallace
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