## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(ggplot2) theme_set(theme_classic()) ## ----load-libraries, message=FALSE, warning=FALSE----------------------------- library(schex) library(dplyr) library(Seurat) ## ----------------------------------------------------------------------------- pbmc_small ## ----umap, message=FALSE, warning=FALSE--------------------------------------- set.seed(10) pbmc_small <- RunUMAP(pbmc_small, dims=1:10, verbose = FALSE) ## ----calc-hexbin-------------------------------------------------------------- pbmc_small <- make_hexbin(pbmc_small, nbins = 10, dimension_reduction = "UMAP") ## ----plot-density, fig.height=7, fig.width=7---------------------------------- plot_hexbin_density(pbmc_small) ## ----plot-meta-1, fig.height=7, fig.width=7----------------------------------- plot_hexbin_meta(pbmc_small, col="nCount_RNA", action="median") ## ----plot-gene, fig.height=7, fig.width=7------------------------------------- gene_id <-"CD1C" schex::plot_hexbin_feature(pbmc_small, type="scale.data", feature=gene_id, action="mean", xlab="UMAP1", ylab="UMAP2", title=paste0("Mean of ", gene_id)) ## ----------------------------------------------------------------------------- gene_id <-"CD1C" gg <- schex::plot_hexbin_feature(pbmc_small, type="scale.data", feature=gene_id, action="mean", xlab="UMAP1", ylab="UMAP2", title=paste0("Mean of ", gene_id)) gg + theme_void() ## ----eval=FALSE--------------------------------------------------------------- # ggsave(gg, file="schex_plot.pdf")