locus_plot | R Documentation |
Plot results for a selected locus
locus_plot(That, ann, cgs, locus.chr, locus.start, locus.end, locus.name = sprintf("%s:%d-%d", locus.chr, locus.start, locus.end), locus.forward = FALSE, flank.start = 1000, flank.end = 1000, comp.cols = rainbow(ncol(That)), legend.pos = "topleft", Tstar = NULL, D = NULL, plot.genes = FALSE, ann.genes = NULL)
That |
a matrix of LMCs |
ann |
CpG annotation |
cgs |
indices of CpGs data for which are present in That with respect to ann |
locus.chr |
chromosome |
locus.start |
start coordinate |
locus.end |
end coordinate |
flank.start |
number of basepairs to extend the locus upstream |
flank.end |
number of basepairs to extend the locus downstream |
comp.cols |
color code for LMCs |
legend.pos |
location of the legend, in accordance with legend |
Tstar |
matrix of reference profiles |
D |
matrix of input methylation data used to produce That |
plot.genes |
if |
ann.genes |
gene annotation necessary for the gene plotting @author Pavlo Lutsik, with modifications by Michael Scherer @export |
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