## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("MerfishData") ## ----message = FALSE---------------------------------------------------------- library(MerfishData) library(ExperimentHub) library(ggpubr) ## ----------------------------------------------------------------------------- eh <- ExperimentHub() query(eh, c("MerfishData", "hypothalamus")) ## ----message = FALSE---------------------------------------------------------- spe <- MouseHypothalamusMoffitt2018() spe ## ----------------------------------------------------------------------------- assay(spe)[1:5,1:5] assay(spe, "molecules")["Aldh1l1",1] colData(spe) head(spatialCoords(spe)) ## ----------------------------------------------------------------------------- table(spatialCoords(spe)[,"z"]) ## ----------------------------------------------------------------------------- table(spe$cell_class) ## ----------------------------------------------------------------------------- relz <- c(0.26, 0.16, 0.06, -0.04, -0.14, -0.24) cdat <- data.frame(colData(spe), spatialCoords(spe)) cdat <- subset(cdat, cell_class != "Ambiguous") cdat$cell_class <- sub(" [1-4]$", "", cdat$cell_class) cdat <- subset(cdat, z %in% relz) cdat$z <- as.character(cdat$z) zum <- paste(0:5 * 100, "um") names(zum) <- as.character(relz) cdat$z <- unname(zum[cdat$z]) ## ----fig.wide = TRUE, fig.width = 10, fig.height = 10------------------------- pal <- get_palette("simpsons", 9) names(pal) <- c("Endothelial", "Excitatory", "OD Immature", "Astrocyte", "Mural", "Microglia", "Ependymal", "Inhibitory", "OD Mature") ggscatter(cdat, x = "x", y = "y", color = "cell_class", facet.by = "z", shape = 20, size = 1, palette = pal) + guides(color = guide_legend(override.aes = list(size = 3))) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()