## ----样式-Knitr，eval = true，echo = false，结果=“ asis” -------------------------------------------------------------------------------------------------------- BiocStyle :: lastx（）## ---- inclage = false -------------------------------------------------------------------------------------------------------------------------------------------------------------库（Knitr）opts_chunk $ set（concordance = true，background =“＃f3f3ff）”）## --------------------------------------------------------------------------------------------------------------------------------------------------库（SIMLR）数据（buettnerflorian）数据（Zeiselamit）#​​# ---- igraph，结果='hide'，消息= false -------------------------------------------------------------------------------------------------------------------------------------------------库（igraph）## ---- simlr_run，警告= false ----------------------------------------------------------------------------------------------------------------- set.seed(11111) example = SIMLR(X = BuettnerFlorian$in_X, c = BuettnerFlorian$n_clust, cores.比率= 0）## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- nmi_1 = compare(BuettnerFlorian$true_labs[,1], example$y$cluster, method="nmi") nmi_1## ----图像，图。show='hide'，图。width = 5，图。示例$ 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 similr 2d for buettnerrian for Buettnerrian for Buettnerflorian”--- simlr_feature_ranking_run，结果='hide'-------------------------------------------------------------种子（11111）等级= simlr_feature_ranking（a = buettnerflorian $ susticy $ s，x = buettnerflorian $ in_x）## ------------------------------------------------------------------------------------------------------------------头（排名$ PVAL）头（排名$ aggr）## ----------------------------------------------------------------------------------------------------------------- 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())