## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) library(gridExtra) ## ---- message = FALSE--------------------------------------------------------- library(corral) library(SingleCellExperiment) library(ggplot2) library(DuoClustering2018) zm4eq.sce <- sce_full_Zhengmix4eq() zm8eq <- sce_full_Zhengmix8eq() ## ----------------------------------------------------------------------------- zm4eq.sce table(colData(zm4eq.sce)$phenoid) ## ----------------------------------------------------------------------------- zm4eq.sce <- corral(inp = zm4eq.sce, whichmat = 'counts') zm4eq.sce ## ----------------------------------------------------------------------------- plot_embedding_sce(sce = zm4eq.sce, which_embedding = 'corral', plot_title = 'corral on Zhengmix4eq', color_attr = 'phenoid', color_title = 'cell type', saveplot = FALSE) ## ----------------------------------------------------------------------------- library(scater) library(gridExtra) # so we can arrange the plots side by side zm4eq.sce <- runUMAP(zm4eq.sce, dimred = 'corral', name = 'corral_UMAP') zm4eq.sce <- runTSNE(zm4eq.sce, dimred = 'corral', name = 'corral_TSNE') ggplot_umap <- plot_embedding_sce(sce = zm4eq.sce, which_embedding = 'corral_UMAP', plot_title = 'Zhengmix4eq corral with UMAP', color_attr = 'phenoid', color_title = 'cell type', returngg = TRUE, showplot = FALSE, saveplot = FALSE) ggplot_tsne <- plot_embedding_sce(sce = zm4eq.sce, which_embedding = 'corral_TSNE', plot_title = 'Zhengmix4eq corral with tSNE', color_attr = 'phenoid', color_title = 'cell type', returngg = TRUE, showplot = FALSE, saveplot = FALSE) gridExtra::grid.arrange(ggplot_umap, ggplot_tsne, ncol = 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()