## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("NewWave") ## ----------------------------------------------------------------------------- suppressPackageStartupMessages( {library(SingleCellExperiment) library(splatter) library(irlba) library(Rtsne) library(ggplot2) library(mclust) library(NewWave)} ) ## ----------------------------------------------------------------------------- params <- newSplatParams() N=500 set.seed(1234) data <- splatSimulateGroups(params,batchCells=c(N/2,N/2), group.prob = rep(0.1,10), de.prob = 0.2, verbose = FALSE) ## ----------------------------------------------------------------------------- set.seed(12359) hvg <- rowVars(counts(data)) names(hvg) <- rownames(counts(data)) data <- data[names(sort(hvg,decreasing=TRUE))[1:500],] ## ----------------------------------------------------------------------------- colData(data) ## ----------------------------------------------------------------------------- data$Batch <- as.factor(data$Batch) ## ----------------------------------------------------------------------------- pca <- prcomp_irlba(t(counts(data)),n=10) plot_data <-data.frame(Rtsne(pca$x)$Y) ## ----------------------------------------------------------------------------- plot_data$batch <- data$Batch plot_data$group <- data$Group ## ----------------------------------------------------------------------------- ggplot(plot_data, aes(x=X1,y=X2,col=group, shape=batch))+ geom_point() ## ----------------------------------------------------------------------------- res <- newWave(data,X = "~Batch", K=10, verbose = TRUE) ## ----------------------------------------------------------------------------- res2 <- newWave(data,X = "~Batch", K=10, verbose = TRUE, children=2) ## ----------------------------------------------------------------------------- res3 <- newWave(data,X = "~Batch", verbose = TRUE,K=10, children=2, n_gene_disp = 100, n_gene_par = 100, n_cell_par = 100) ## ----------------------------------------------------------------------------- res3 <- newWave(data,X = "~Batch", verbose = TRUE,K=10, children=2, n_gene_par = 100, n_cell_par = 100, commondispersion = FALSE) ## ----------------------------------------------------------------------------- latent <- reducedDim(res) tsne_latent <- data.frame(Rtsne(latent)$Y) tsne_latent$batch <- data$Batch tsne_latent$group <- data$Group ## ----------------------------------------------------------------------------- ggplot(tsne_latent, aes(x=X1,y=X2,col=group, shape=batch))+ geom_point() ## ----------------------------------------------------------------------------- cluster <- kmeans(latent, 10) adjustedRandIndex(cluster$cluster, data$Group) ## ----------------------------------------------------------------------------- sessionInfo()