## ----------------------------------------------------------------------------- suppressPackageStartupMessages({ library(ExperimentHub) library(SingleCellExperiment) library(DuoClustering2018) library(plyr) }) ## ----------------------------------------------------------------------------- eh <- ExperimentHub() query(eh, "DuoClustering2018") ## ----------------------------------------------------------------------------- eh[["EH1500"]] ## ----------------------------------------------------------------------------- sce_filteredExpr10_Koh() ## ----------------------------------------------------------------------------- res <- plyr::rbind.fill( clustering_summary_filteredExpr10_Koh_v2(), clustering_summary_filteredHVG10_Koh_v2(), clustering_summary_filteredExpr10_Zhengmix4eq_v2(), clustering_summary_filteredHVG10_Zhengmix4eq_v2() ) dim(res) ## ----------------------------------------------------------------------------- head(res) ## ----------------------------------------------------------------------------- method_colors <- c(CIDR = "#332288", FlowSOM = "#6699CC", PCAHC = "#88CCEE", PCAKmeans = "#44AA99", pcaReduce = "#117733", RtsneKmeans = "#999933", Seurat = "#DDCC77", SC3svm = "#661100", SC3 = "#CC6677", TSCAN = "grey34", ascend = "orange", SAFE = "black", monocle = "red", RaceID2 = "blue") ## ----------------------------------------------------------------------------- perf <- plot_performance(res, method_colors = method_colors) names(perf) perf$median_ari_vs_k perf$median_ari_heatmap_truek ## ----------------------------------------------------------------------------- stab <- plot_stability(res, method_colors = method_colors) names(stab) stab$stability_vs_k stab$stability_heatmap_truek ## ---- fig.height = 8---------------------------------------------------------- entr <- plot_entropy(res, method_colors = method_colors) names(entr) entr$entropy_vs_k entr$normentropy ## ---- fig.height = 8---------------------------------------------------------- timing <- plot_timing(res, method_colors = method_colors, scaleMethod = "RtsneKmeans") names(timing) timing$time_normalized_by_ref ## ---- fig.height = 8---------------------------------------------------------- kdiff <- plot_k_diff(res, method_colors = method_colors) names(kdiff) kdiff$diff_kest_ktrue ## ----------------------------------------------------------------------------- sessionInfo()