## ----echo = FALSE, message = FALSE---------------------------------------------------------------- library(knitr) knitr::opts_chunk$set( error = FALSE, warning = FALSE, message = FALSE) ## ------------------------------------------------------------------------------------------------- library(EnrichedHeatmap) load(system.file("extdata", "neg_cr.RData", package = "EnrichedHeatmap")) all_genes = all_genes[unique(neg_cr$gene)] all_tss = promoters(all_genes, upstream = 0, downstream = 1) mat_neg_cr = normalizeToMatrix(neg_cr, all_tss, mapping_column = "gene", w = 50, mean_mode = "w0") ## ----eval = FALSE--------------------------------------------------------------------------------- # EnrichedHeatmap(mat_neg_cr, name = "neg_cr", col = c("white", "darkgreen"), # top_annotation = HeatmapAnnotation(enrich = anno_enriched(gp = gpar(col = "darkgreen"))), # row_title = "by default enriched scores") # # EnrichedHeatmap(mat_neg_cr, name = "neg_cr", col = c("white", "darkgreen"), # top_annotation = HeatmapAnnotation(enrich = anno_enriched(gp = gpar(col = "darkgreen"))), # cluster_rows = TRUE, # row_title = "by hierarchcal clustering + Euclidean distance\ndendrogram reordered by enriched scores") # # EnrichedHeatmap(mat_neg_cr, name = "neg_cr", col = c("white", "darkgreen"), # top_annotation = HeatmapAnnotation(enrich = anno_enriched(gp = gpar(col = "darkgreen"))), # cluster_rows = TRUE, clustering_distance_rows = dist_by_closeness, # row_title = "by hierarchcal clustering + closeness distance\ndendrogram reordered by enriched scores") ## ----echo = FALSE, fig.width = 8, fig.height = 6-------------------------------------------------- gb1 = grid.grabExpr(draw(EnrichedHeatmap(mat_neg_cr, name = "neg_cr", col = c("white", "darkgreen"), top_annotation = HeatmapAnnotation(enrich = anno_enriched(gp = gpar(col = "darkgreen"))), row_title = "\nby default enriched scores"))) gb2 = grid.grabExpr(draw(EnrichedHeatmap(mat_neg_cr, name = "neg_cr", col = c("white", "darkgreen"), top_annotation = HeatmapAnnotation(enrich = anno_enriched(gp = gpar(col = "darkgreen"))), cluster_rows = TRUE, row_title = "by hierarchcal clustering + Euclidean distance\ndendrogram reordered by enriched scores"))) load(system.file("extdata", "neg_cr_order_by_dist_closeness.RData", package = "EnrichedHeatmap")) gb3 = grid.grabExpr(draw(EnrichedHeatmap(mat_neg_cr, name = "neg_cr", col = c("white", "darkgreen"), top_annotation = HeatmapAnnotation(enrich = anno_enriched(gp = gpar(col = "darkgreen"))), cluster_rows = FALSE, row_order = row_order, row_title = "by hierarchcal clustering + closeness distance\ndendrogram reordered by enriched scores"))) grid.newpage() pushViewport(viewport(x = 0, width = 1/3, just = "left")) grid.draw(gb1) popViewport() pushViewport(viewport(x = 1/3, width = 1/3, just = "left")) grid.draw(gb2) popViewport() pushViewport(viewport(x = 2/3, width = 1/3, just = "left")) grid.draw(gb3) popViewport()