## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # BiocManager::install("Dune") ## ----setup-------------------------------------------------------------------- suppressPackageStartupMessages({ library(RColorBrewer) library(dplyr) library(ggplot2) library(tidyr) library(knitr) library(purrr) library(Dune) }) data("nuclei", package = "Dune") theme_set(theme_classic()) ## ----------------------------------------------------------------------------- ggplot(nuclei, aes(x = x, y = y, col = subclass_label)) + geom_point() ## ----fig.hold='hold', out.width="33%", fig.height=9--------------------------- walk(c("SC3", "Seurat", "Monocle"), function(clus_algo){ df <- nuclei df$clus_algo <- nuclei[, clus_algo] p <- ggplot(df, aes(x = x, y = y, col = as.character(clus_algo))) + geom_point(size = 1.5) + # guides(color = FALSE) + labs(title = clus_algo, col = "clusters") + theme(legend.position = "bottom") print(p) }) ## ----------------------------------------------------------------------------- plotARIs(nuclei %>% select(SC3, Seurat, Monocle)) ## ----------------------------------------------------------------------------- merger <- Dune(clusMat = nuclei %>% select(SC3, Seurat, Monocle), verbose = TRUE) ## ----------------------------------------------------------------------------- names(merger) ## ----------------------------------------------------------------------------- plotARIs(clusMat = merger$currentMat) ## ----------------------------------------------------------------------------- plotPrePost(merger) ## ----------------------------------------------------------------------------- ConfusionPlot(merger$initialMat[, "SC3"], merger$currentMat[, "SC3"]) + labs(x = "Before merging", y = "After merging") ## ----------------------------------------------------------------------------- ARItrend(merger) ## ----------------------------------------------------------------------------- sessionInfo()