## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"----------------------------- BiocStyle::latex() ## ----include=FALSE------------------------------------------------------------------ library(knitr) opts_chunk$set( concordance = TRUE, background = "#f3f3ff" ) ## ----req---------------------------------------------------------------------------- library(SIMLR) data(BuettnerFlorian) data(ZeiselAmit) ## ----igraph, results='hide', message=FALSE------------------------------------------ library(igraph) ## ----SIMLR_run, warning=FALSE------------------------------------------------------- set.seed(11111) example = SIMLR(X = BuettnerFlorian$in_X, c = BuettnerFlorian$n_clust, cores.ratio = 0) ## ----nmi_performance---------------------------------------------------------------- nmi_1 = compare(BuettnerFlorian$true_labs[,1], example$y$cluster, method="nmi") nmi_1 ## ----image, fig.show='hide', fig.width=5, fig.height=5,results='hide'--------------- plot(example$ydata, col = c(topo.colors(BuettnerFlorian$n_clust))[BuettnerFlorian$true_labs[,1]], xlab = "SIMLR component 1", ylab = "SIMLR component 2", pch = 20, main="SIMILR 2D visualization for BuettnerFlorian") ## ----SIMLR_Feature_Ranking_run, results='hide'-------------------------------------- set.seed(11111) ranks = SIMLR_Feature_Ranking(A=BuettnerFlorian$results$S,X=BuettnerFlorian$in_X) ## ----head-ranks--------------------------------------------------------------------- head(ranks$pval) head(ranks$aggR) ## ----SIMLR_Large_Scale_run, warning=FALSE------------------------------------------- set.seed(11111) example_large_scale = SIMLR_Large_Scale(X = ZeiselAmit$in_X, c = ZeiselAmit$n_clust, kk = 10) ## ----nmi_performance_large_scale---------------------------------------------------- nmi_2 = compare(ZeiselAmit$true_labs[,1], example_large_scale$y$cluster, method="nmi") nmi_2 ## ----image_large_scale, fig.show='hide', fig.width=5, fig.height=5,results='hide'---- plot(example_large_scale$ydata, col = c(topo.colors(ZeiselAmit$n_clust))[ZeiselAmit$true_labs[,1]], xlab = "SIMLR component 1", ylab = "SIMLR component 2", pch = 20, main="SIMILR 2D visualization for ZeiselAmit") ## ----SIMLR_Number_Clusters_run, warning=FALSE--------------------------------------- set.seed(53900) NUMC = 2:5 res_example = SIMLR_Estimate_Number_of_Clusters(BuettnerFlorian$in_X, NUMC = NUMC, cores.ratio = 0) ## ----SIMLR_NC_output_k1------------------------------------------------------------- NUMC[which.min(res_example$K1)] ## ----SIMLR_NC_output_k2------------------------------------------------------------- NUMC[which.min(res_example$K2)] ## ----SIMLR_NC_output, warning=FALSE------------------------------------------------- res_example ## ----sessioninfo, results='asis', echo=FALSE---------------------------------------- toLatex(sessionInfo())