gseaPlot.R
#' @param m matrix n x m
#' @param groups vector of size n of numbers from 1 to k
#' @return matrix k*m of column averages by groups
colMeansByGroups <- function(m, groups) {
x <- Matrix::sparseMatrix(j=seq_along(groups),
i=groups,
x=rep(1, length(groups)))
z <- x %*% m
res <- sweep(z, 1, table(groups), "/")
}
rasterizeHeatmap <- function(m, palette=palette, maxDimensions=c(2500, 1000)) {
mr <- round((m - min(m))/(max(m)-min(m)) * (length(palette) - 1) + 1)
cap <- matrix(palette[as.matrix(mr)], nrow=nrow(m))
repN <- floor(maxDimensions/dim(m))
cap1 <- matrix(rep(t(cap), each=repN[2]), nrow=nrow(cap), byrow = TRUE)
cap2 <- matrix(rep(cap1, each=repN[1]), ncol=ncol(cap1), byrow = FALSE)
# cap2[repN[1], repN[2]] == cap[1,1]
# cap2[repN[1]+1, repN[2]] == cap[2,1]
# cap2[repN[1], repN[2]+1] == cap[1,2]
# cap2[repN[1]+1, repN[2]+1] == cap[2,2]
res <- rasterGrob(cap2,
width=unit(1, "npc"), height=unit(1, "npc"),
interpolate = FALSE)
res
}
#' 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)
#' @param pallete a vector of colors to draw heatmap
#' @param annotationColors a list of colors to use in annotation
#' @return path to an svg file
#' @importFrom fgsea plotEnrichment fgseaMultilevel
#' @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,
annotationColors=NULL,
pallete=c("blue", "white", "red")) {
fullPalette <- colorRampPalette(pallete)(50)
featureData <- fData(es)
colnames(featureData) <- fvarLabels(es)
absEps <- 1e-10
ranks <- featureData[, rankBy]
if (!is.numeric(ranks)) {
ranks <- as.numeric(ranks)
}
names(ranks) <- as.character(seq_along(ranks))
pathway <- as.character(selectedGenes)
system.time(
fgseaRes <- fgseaMultilevel(list(p=pathway), ranks, sampleSize = 101, nproc=1, absEps = absEps/2)
)
pvalString <- if (fgseaRes$pval < absEps) {
sprintf("<%.2g", absEps)
} else {
sprintf("\u2248%.2g", fgseaRes$pval)
}
labelString <- sprintf("p-value%s, NES=%.2f", pvalString, fgseaRes$NES)
p <- plotEnrichment(pathway, ranks) + ggtitle(NULL, subtitle=labelString)
if (vertical) {
p <- p +
scale_x_reverse(limits=c(length(ranks) + 1, -1), expand=c(0, 0)) +
coord_flip() +
NULL
} else {
p <- p + scale_x_continuous(limits=c(-1, length(ranks) + 1), expand=c(0, 0))
}
p <- p + theme(plot.margin = unit(c(0.5, 0.5, 0.5, 0.5), "cm"))
enrichmentGrob <- ggplotGrob(p)
if (addHeatmap && ncol(es) > 1) {
# preparing heatmap
mat <- exprs(es)[order(ranks, decreasing = TRUE), ]
mat <- t(apply(mat, 1, scales::rescale))
grouping <- ceiling(seq_len(nrow(mat)) / nrow(mat) * 1000)
aggr <- colMeansByGroups(mat, grouping)
annotation_col <- NULL
annotation_colors <- NULL
if (!is.null(showAnnotation)) {
values <- es[[showAnnotation]]
annotation_col <- data.frame(row.names=colnames(es),
setNames(list(factor(values,
levels=unique(values))),
showAnnotation))
if (!is.null(annotationColors)) {
annotation_colors <- list()
annotation_colors[[showAnnotation]] <- as.character(annotationColors)
names(annotation_colors[[showAnnotation]]) <- names(annotationColors)
}
}
# adding column to the left
# 4 -> 1.5
# 6 -> 2
# 20+ -> 3
heatmapWidth <- max(1, 3 - 6/ncol(aggr))
if (vertical) {
heatmapWidth <- min(heatmapWidth, width/4)
ph <- pheatmap::pheatmap(aggr,
cluster_rows = FALSE, cluster_cols = FALSE,
show_rownames = FALSE, show_colnames = FALSE,
color=fullPalette,
annotation_col = annotation_col,
annotation_colors = annotation_colors,
legend = FALSE,
silent = TRUE)
heatmapGrobs <- ph$gtable
hgMatrix <- rasterizeHeatmap(aggr,
palette=fullPalette,
maxDimensions=c(2500, 1000))
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=fullPalette,
annotation_row = annotation_col,
annotation_colors = annotation_colors,
legend = FALSE,
silent = TRUE)
heatmapGrobs <- ph$gtable
hgMatrix <- rasterizeHeatmap(Matrix::t(aggr),
palette=fullPalette,
maxDimensions=c(1000, 2500))
panel_id <- enrichmentGrob$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)
}
