## ----设置，包括= false -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) library(gridExtra) ## ---- message = FALSE--------------------------------------------------------- library(corral) library（SingleCellexperiment）库（GGPLOT2）库（DuoClustering2018）Zm4eq.sce <-sce_full_zhengmix4eq（）---------------------------------------------------------------------------------------- ZM4EQ.SCE表（Coldata（ZM4EQ.SCE）$ facoid）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------- zm4eq.sce在------------------------------------------------ plot_embedding_sce(sce = zm4eq.sce，whe_embedding ='Corral'，plot_title ='corral on zhengmix4eq'，color_attr ='fanttr ='fansoid'，color_title ='cell type'，saveplot = false）-------------------------------------------------------------------------------------------------------图书馆（Sconter）library（gridextra）＃因此，我们可以并排排列ZM4EQ.SCE <-runumap（zm4eq.sce，dimred ='Corral'，name ='Corral_umap'）'Corral'，name ='Corral_tsne'）ggplot_umap <-plot_embedding_sce（sce = zm4eq.sce，what_embedding ='corral_umap'，plot_title ='zhengengmix4eq corral with umap with umap'with umap'= true，showplot = false，saveplot = false）ggplot_tsne <-plot_embedding_sce（sce = zm4eq.sce，what_embedding ='corral_tsne'，plot_title ='zhengmix4eq corral with with with with tsnereturngg = true，showplot = false，saveplot = false）乘数（ggplot_umap，ggplot_tsne，cols = 2）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- zm4eq.countmat <- assay(zm4eq.sce,'counts') zm4eq.countcorral <- corral(zm4eq.countmat) ## ----------------------------------------------------------------------------- zm4eq.countcorral ## ----------------------------------------------------------------------------- celltype_vec <- zm4eq.sce$phenoid plot_embedding(embedding = zm4eq.countcorral$v, plot_title = 'corral on Zhengmix4eq', color_vec = celltype_vec, color_title = 'cell type', saveplot = FALSE) ## ----------------------------------------------------------------------------- zm8eq.corral <- corral(zm8eq, fullout = TRUE) zm8eq.corralsmooth <- corral(zm8eq, fullout = TRUE, smooth = TRUE) ## ----------------------------------------------------------------------------- gene_names <- rowData(zm4eq.sce)$symbol biplot_corral(corral_obj = zm4eq.countcorral, color_vec = celltype_vec, text_vec = gene_names) ## ----------------------------------------------------------------------------- sessionInfo()