#' @export
# The same as phenotypePlot, but uses ggrepel to keep labels from overlapping.
phenotype_plot <-
function(d, max.y,max.x, suggestive.line, significant.line,
size.x.labels=9, size.y.labels=9, switch.axis=F, sort.by.value=F, sort.by.category.value=F,
#annotation
annotate.phenotype.description,
annotate.angle=30, annotate.size=5, annotate.level,
annotate.phenotype=F,
annotate.snp.w.phenotype=F,
annotate.snp=F, annotate.snp.angle=0,
annotate.list, annotate.only.largest=T,
#labels
lc.labels=F,
x.group.labels=T, x.phenotype.labels=F,
sizes=F, direction=F, point.size=3,
#plot characteristics
use.color=T,
color.palette,
title= paste0("Phenotype Plot ", date()),
x.axis.label="Phenotypes",
y.axis.label="Values",
y.axis.interval=5) {
phenotypePlot(d,max.y,max.x, suggestive.line, significant.line,
size.x.labels, size.y.labels, switch.axis, sort.by.value, sort.by.category.value,
#annotation
annotate.phenotype.description,
annotate.angle, annotate.size, annotate.level,
annotate.phenotype,
annotate.snp.w.phenotype,
annotate.snp, annotate.snp.angle,
annotate.list, annotate.only.largest,
#labels
lc.labels,
x.group.labels, x.phenotype.labels,
sizes, direction, point.size,
#plot characteristics
use.color,
color.palette,
title,
x.axis.label,
y.axis.label,
y.axis.interval)
}
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