## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) library(gridExtra) ## ---- message = FALSE--------------------------------------------------------- library(corral) library(SingleCellExperiment) library(ggplot2) library(CellBench) library(MultiAssayExperiment) scmix_dat <- load_all_data()[1:3] ## ----------------------------------------------------------------------------- scmix_dat ## ----------------------------------------------------------------------------- platforms <- c('10X','CELseq2','Dropseq') for(i in seq_along(scmix_dat)) { colData(scmix_dat[[i]])$Method<- rep(platforms[i], ncol(scmix_dat[[i]])) } scmix_mae <- as(scmix_dat,'MultiAssayExperiment') scmix_dat <- as.list(MultiAssayExperiment::experiments(MultiAssayExperiment::intersectRows(scmix_mae))) ## ----------------------------------------------------------------------------- colData(scmix_dat[[2]])$non_ERCC_percent <- NULL # need to remove this column so the objects can be concatenated scmix_sce <- SingleCellExperiment::cbind(scmix_dat[[1]], scmix_dat[[2]], scmix_dat[[3]]) ## ----------------------------------------------------------------------------- scmix_sce <- corralm(scmix_sce, splitby = 'Method') ## ----------------------------------------------------------------------------- plot_embedding_sce(sce = scmix_sce, which_embedding = 'corralm', color_attr = 'Method', color_title = 'platform', ellipse_attr = 'cell_line', plot_title = 'corralm on scmix', saveplot = FALSE) ## ----------------------------------------------------------------------------- scmix_matlist <- sce2matlist(sce = scmix_sce, splitby = 'Method', whichmat = 'counts') # for plotting purposes later, while we're here platforms <- colData(scmix_sce)$Method cell_lines <- colData(scmix_sce)$cell_line ## ----------------------------------------------------------------------------- scmix_corralm <- corralm(scmix_matlist) scmix_corralm plot_embedding(embedding = scmix_corralm$v, plot_title = 'corralm on scmix', color_vec = platforms, color_title = 'platform', ellipse_vec = cell_lines, saveplot = FALSE) ## ----------------------------------------------------------------------------- sessionInfo()