## ----------------------------------------------------------------------------- library(ExperimentHub) eh <- ExperimentHub() query(eh, "spatialDmelxsim") ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(SummarizedExperiment)) library(spatialDmelxsim) se <- spatialDmelxsim() ## ----------------------------------------------------------------------------- table(is.na(mcols(se)$paper_symbol)) rownames(se) <- mcols(se)$paper_symbol ## ----------------------------------------------------------------------------- assay(se, "total") <- assay(se, "a1") + assay(se, "a2") assay(se, "ratio") <- assay(se, "a1") / assay(se, "total") ## ----------------------------------------------------------------------------- plotGene <- function(gene) { x <- se$normSlice y <- assay(se, "ratio")[gene,] col <- as.integer(se$rep) plot(x, y, xlab="normSlice", ylab="sim / total ratio", ylim=c(0,1), main=gene, col=col) lw <- loess(y ~ x, data=data.frame(x,y=unname(y))) lines(sort(lw$x), lw$fitted[order(lw$x)], col="red", lwd=2) abline(h=0.5, col="grey") } ## ----DOR---------------------------------------------------------------------- plotGene("DOR") ## ----uif---------------------------------------------------------------------- plotGene("uif") ## ----bmm---------------------------------------------------------------------- plotGene("bmm") ## ----hb----------------------------------------------------------------------- plotGene("hb") ## ----CG4500------------------------------------------------------------------- plotGene("CG4500") ## ----------------------------------------------------------------------------- sessionInfo()