## ----echo=FALSE, results="hide"----------------------------------------------- knitr::opts_chunk$set(error=FALSE, warning=FALSE, message=FALSE) ## ----getPackage, eval=FALSE--------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("MouseGastrulationData") ## ----Load, message=FALSE------------------------------------------------------ library(MouseGastrulationData) ## ----------------------------------------------------------------------------- head(AtlasSampleMetadata, n = 3) ## ----message=FALSE------------------------------------------------------------ sce <- EmbryoAtlasData(samples = 21) sce ## ----------------------------------------------------------------------------- counts(sce)[6:9, 1:3] ## ----------------------------------------------------------------------------- head(sizeFactors(sce)) ## ----------------------------------------------------------------------------- head(rowData(sce)) ## ----------------------------------------------------------------------------- head(colData(sce)) ## ----fig.height = 6----------------------------------------------------------- #exclude technical artefacts singlets <- which(!(colData(sce)$doublet | colData(sce)$stripped)) plot( x = reducedDim(sce, "umap")[singlets, 1], y = reducedDim(sce, "umap")[singlets, 2], col = EmbryoCelltypeColours[colData(sce)$celltype[singlets]], pch = 19, xaxt = "n", yaxt = "n", xlab = "UMAP1", ylab = "UMAP2" ) ## ----message = FALSE---------------------------------------------------------- sce <- EmbryoAtlasData(samples=21, get.spliced=TRUE) names(assays(sce)) ## ----------------------------------------------------------------------------- unfilt <- EmbryoAtlasData(type="raw", samples=c(1:2)) sapply(unfilt, dim) ## ----------------------------------------------------------------------------- sessionInfo()