#' Plot the result of the slidingWindow algorithm.
#' @export
plot.complexFeaturesSW <- function(sw.result, protein.traces.long, n.largest=NULL,
log=FALSE) {
subgroups.dt <- sw.result$subgroups.dt
complex.id <- unique(protein.traces.long$complex_id)
trace.plot <- plotTraces(protein.traces.long,
'protein_id', 'complex_id',
paste('Protein traces of complex', complex.id),
plot=F,
log=log)
if (!is.null(n.largest)) {
n.subunits <- unique(subgroups.dt$n_subunits)
n.subunits.ord <- n.subunits[order(n.subunits, decreasing=TRUE)]
largest.n <- head(n.subunits.ord, n.largest)
subgroups.dt <- subgroups.dt[n_subunits %in% largest.n]
}
subgroup.plot <- ggplot(subgroups.dt) +
geom_point(aes(x=sec, y=protein_id, color=protein_id),
size=2, shape=15) +
xlim(c(min(protein.traces.long$sec), max(protein.traces.long$sec))) +
facet_wrap(~ subgroup, nrow=length(unique(subgroups.dt$subgroup))) +
ggtitle(sprintf('Detected subgroups (window size = %d, correlation cutoff = %f)',
sw.result$window.size, sw.result$corr.cutoff)) +
theme(axis.line.y=element_blank()
# axis.text.y=element_blank(),
# axis.ticks.y=element_blank(),
# axis.title.y=element_blank()
# panel.background=element_blank(),
# panel.border=element_blank(),
# panel.grid.major=element_blank(),
# panel.grid.minor=element_blank(),
# plot.background=element_blank()
)
p <- multiplot(trace.plot + ylim(c(0, 5e06)),
subgroup.plot)
print(p)
p
}
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