Custom visualization showing cell density in an embedding

[ycl6]

A request received recently to show cell density in a TSNE/UMAP plot, will be nice to have a function in scRUtils to produce different variations of this.

    suppressPackageStartupMessages({
        library(scater)
        library(scRNAseq)
    })

    sce <- ZeiselBrainData()
    
    sce <- logNormCounts(sce)
    sce <- runPCA(sce)

    set.seed(1000)
    sce <- runTSNE(sce, perplexity=50, dimred="PCA", n_dimred=20)
    tsne = as.data.frame(reducedDim(sce, "TSNE"))
    colnames(tsne) = c("Dim1","Dim2")
    tsne$tissue = sce$tissue

    # Version 1
    a = ggplot(tsne, aes(x = Dim1, y = Dim2)) +
        geom_density_2d_filled(n = 50) + facet_wrap(vars(tissue), ncol = 1) +
        scale_fill_brewer("Cell\nDensity",palette = "Spectral", direction = -1)

    # Version 2
    b = ggplot(tsne, aes(x = Dim1, y = Dim2)) + geom_point(size = 1, alpha = 0.2) +
        geom_density_2d(aes(color = after_stat(level), linewidth = after_stat(level)), n = 50) + 
        facet_wrap(vars(tissue), ncol = 1) + scale_linewidth("Cell\nDensity", range = c(0.5, 1.5)) +
        scale_color_distiller("Cell\nDensity", palette = "Spectral", direction = -1)

    cowplot::plot_grid(a, b, labels = c('V1', 'V2'))

^{Created on 2024-03-08 with reprex v2.1.0}