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166 | #' Returns path to an svg file with enrichment plot
#' @param es ExpressionSet object.
#' @param rankBy name of the numeric column used for gene ranking
#' @param selectedGenes indexes of selected genes (starting from one, in the order of fData)
#' @param width width of the image (in inches)
#' @param height height of the image (in inches)
#' @param vertical whether to use vertical orientation (default: FALSE)
#' @param addHeatmap whether to add an expression heatmap, sorted by rankBy (default: FALSE)
#' @param showAnnotation a name of column annotation to add to the heatmap, default: NULL (no annotation)
#' @return path to an svg file
#' @importFrom fgsea plotEnrichment fgsea
#' @importFrom ggplot2 ggtitle
#' @importFrom grDevices colorRampPalette dev.off svg
#' @importFrom utils head
#' @import grid
#' @import gtable
#' @import svglite
#' @import stats
gseaPlot <- function(es, rankBy, selectedGenes, width, height,
vertical=FALSE,
addHeatmap=FALSE,
showAnnotation=NULL) {
featureData <- fData(es)
colnames(featureData) <- fvarLabels(es)
ranks <- featureData[, rankBy]
if (!is.numeric(ranks)) {
ranks <- as.numeric(ranks)
}
names(ranks) <- as.character(seq_along(ranks))
pathway <- as.character(selectedGenes)
fgseaRes <- fgsea(list(pathway), ranks, nperm=2000, nproc=1)
pvalString <- if (fgseaRes$nMoreExtreme == 0) {
"<1e-3"
} else {
sprintf("=%.2g", fgseaRes$pval)
}
labelString <- sprintf("p-value%s, NES=%.2f", pvalString, fgseaRes$NES)
p <- plotEnrichment(pathway, ranks) + ggtitle(NULL, subtitle=labelString)
if (vertical) {
p <- p +
scale_x_reverse(limits=c(length(ranks) + 1, -1), expand=c(0, 0)) +
coord_flip() +
NULL
} else {
p <- p + scale_x_continuous(limits=c(-1, length(ranks) + 1), expand=c(0, 0))
}
p <- p + theme(plot.margin = unit(c(0.5, 0.5, 0.5, 0.5), "cm"))
enrichmentGrob <- ggplotGrob(p)
if (addHeatmap) {
# preparing heatmap
mat <- exprs(es)[order(ranks, decreasing = TRUE), ]
mat <- t(apply(mat, 1, scales::rescale))
grouping <- ceiling(seq_len(nrow(mat)) / nrow(mat) * 1000)
aggr <- Matrix.utils::aggregate.Matrix(mat, groupings=grouping, fun="mean")
annotation_col <- NULL
if (!is.null(showAnnotation)) {
values <- es[[showAnnotation]]
annotation_col <- data.frame(row.names=colnames(es),
setNames(list(factor(values,
levels=unique(values))),
showAnnotation))
}
# adding column to the left
# 4 -> 1.5
# 6 -> 2
# 20+ -> 3
heatmapWidth <- max(1, 3 - 6/ncol(aggr))
if (vertical) {
heatmapWidth <- min(heatmapWidth, width/4)
ph <- pheatmap::pheatmap(aggr,
cluster_rows = FALSE, cluster_cols = FALSE,
show_rownames = FALSE, show_colnames = FALSE,
color=colorRampPalette(c("blue", "white", "red"))(50),
annotation_col = annotation_col,
legend = FALSE,
silent = TRUE)
heatmapGrobs <- ph$gtable
hgMatrix <- heatmapGrobs$grobs[[head(which(heatmapGrobs$layout$name == "matrix"), 1)]]
panel_id <- enrichmentGrob$layout[enrichmentGrob$layout$name == "panel",c("t","l")]
enrichmentGrob <- gtable_add_cols(enrichmentGrob, unit(heatmapWidth, "inch"), 0)
enrichmentGrob <- gtable_add_grob(enrichmentGrob, hgMatrix,
t = panel_id$t, l = 1, name="matrix")
if (!is.null(showAnnotation)) {
hgColAnnotation <- heatmapGrobs$grobs[[head(which(heatmapGrobs$layout$name == "col_annotation"), 1)]]
hgAnnotationLegend <- heatmapGrobs$grobs[[head(which(heatmapGrobs$layout$name == "annotation_legend"), 1)]]
hgLegend <- gtable_filter(heatmapGrobs, "annotation_legend", fixed=TRUE, trim=TRUE)
enrichmentGrob <- gtable_add_grob(enrichmentGrob, hgColAnnotation,
t = 1, l = 1, b=panel_id$t-1, name="col_annotation")
enrichmentGrob <- gtable_add_cols(enrichmentGrob, gtable_width(hgLegend), 0)
enrichmentGrob <- gtable_add_grob(enrichmentGrob, hgAnnotationLegend,
t = panel_id$t, l = 1, name="annotation_legend")
}
} else {
# horizontal
heatmapWidth <- min(heatmapWidth, height/4)
ph <- pheatmap::pheatmap(Matrix::t(aggr),
cluster_rows = FALSE, cluster_cols = FALSE,
show_rownames = FALSE, show_colnames = FALSE,
color=colorRampPalette(c("blue", "white", "red"))(50),
annotation_row = annotation_col,
legend = FALSE,
silent = TRUE)
heatmapGrobs <- ph$gtable
hgMatrix <- heatmapGrobs$grobs[[head(which(heatmapGrobs$layout$name == "matrix"), 1)]]
panel_id <- enrichmentGrob$layout[enrichmentGrob$layout$name == "panel",c("t","l")]
enrichmentGrob <- gtable_add_rows(enrichmentGrob, unit(heatmapWidth, "inch"), 0)
enrichmentGrob <- gtable_add_grob(enrichmentGrob, hgMatrix,
t = 1, l=panel_id$l, name="matrix")
if (!is.null(showAnnotation)) {
hgColAnnotation <- heatmapGrobs$grobs[[head(which(heatmapGrobs$layout$name == "row_annotation"), 1)]]
hgAnnotationLegend <- heatmapGrobs$grobs[[head(which(heatmapGrobs$layout$name == "annotation_legend"), 1)]]
hgLegend <- gtable_filter(heatmapGrobs, "annotation_legend", fixed=TRUE, trim=TRUE)
enrichmentGrob <- gtable_add_grob(enrichmentGrob, hgColAnnotation,
t = 1, l = 1, b=1, r=panel_id$l-1, name="col_annotation")
enrichmentGrob <- gtable_add_cols(enrichmentGrob, gtable_width(hgLegend), 0)
enrichmentGrob <- gtable_add_grob(enrichmentGrob, hgAnnotationLegend,
t = 1, l = 1, name="annotation_legend")
}
}
}
f <- tempfile(pattern = "enrichment", tmpdir = getwd(), fileext = ".svg")
svg(f, width=width, height=height)
grid.draw(enrichmentGrob)
dev.off()
# ggsave(p, filename = f, width=width, height=height)
jsonlite::toJSON(f)
}
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