##' @rdname ridgeplot
##' @exportMethod ridgeplot
setMethod("ridgeplot", signature(x = "gseaResult"),
function(x, showCategory = 30, fill = "p.adjust",
core_enrichment = TRUE, label_format = 30, ...) {
ridgeplot.gseaResult(x, showCategory = showCategory,
fill = fill, core_enrichment = core_enrichment,
label_format = label_format, ...)
})
##' @rdname ridgeplot
##' @param orderBy The order of the Y-axis
##' @param decreasing logical. Should the orderBy order be increasing or decreasing?
##' @importFrom ggplot2 scale_fill_gradientn
##' @importFrom ggplot2 aes_string
##' @importFrom ggplot2 scale_x_reverse
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 scale_y_discrete
##' @importFrom rlang check_installed
##' @author Guangchuang Yu
ridgeplot.gseaResult <- function(x, showCategory=30, fill="p.adjust",
core_enrichment = TRUE, label_format = 30,
orderBy = "NES", decreasing = FALSE) {
if (!is(x, "gseaResult"))
stop("currently only support gseaResult")
if (!fill %in% colnames(x@result)) {
stop("'fill' variable not available ...")
}
## geom_density_ridges <- get_fun_from_pkg('ggridges', 'geom_density_ridges')
if (orderBy != 'NES' && !orderBy %in% colnames(x@result)) {
message('wrong orderBy parameter; set to default `orderBy = "NES"`')
orderBy <- "NES"
}
if (inherits(showCategory, 'numeric')) {
selected <- seq_len(showCategory)
} else if (inherits(showCategory, "character")) {
ii <- match(showCategory, x@result$Description)
selected <- x@result[ii, "ID"]
} else {
warning("showCategory should be a number of pathways or a vector of selected pathways")
}
if (core_enrichment) {
gs2id <- geneInCategory(x)[selected]
} else {
gs2id <- x@geneSets[x$ID[selected]]
}
if (x@readable && length(x@gene2Symbol) > 0) {
id <- match(names(x@geneList), names(x@gene2Symbol))
names(x@geneList) <- x@gene2Symbol[id]
}
gs2val <- lapply(gs2id, function(id) {
res <- x@geneList[id]
res <- res[!is.na(res)]
})
nn <- names(gs2val)
i <- match(nn, x$ID)
nn <- x$Description[i]
# j <- order(x$NES[i], decreasing=FALSE)
j <- order(x@result[[orderBy]][i], decreasing = decreasing)
len <- sapply(gs2val, length)
gs2val.df <- data.frame(category = rep(nn, times=len),
color = rep(x[i, fill], times=len),
value = unlist(gs2val))
colnames(gs2val.df)[2] <- fill
gs2val.df$category <- factor(gs2val.df$category, levels=nn[j])
label_func <- default_labeller(label_format)
if(is.function(label_format)) {
label_func <- label_format
}
check_installed('ggridges', 'for `ridgeplot()`.')
ggplot(gs2val.df, aes_string(x="value", y="category", fill=fill)) +
ggridges::geom_density_ridges() +
# scale_fill_continuous(name = fill) +
set_enrichplot_color(type = "fill", name = fill) +
scale_y_discrete(labels = label_func) +
## scale_fill_gradientn(name = fill, colors=sig_palette, guide=guide_colorbar(reverse=TRUE)) +
## geom_vline(xintercept=0, color='firebrick', linetype='dashed') +
xlab(NULL) + ylab(NULL) + theme_dose()
}
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