getDensity: Get local density (z) of bivariate relationship (x,y)

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Get local density (z) of bivariate relationship (x,y)

Description

Get local density (z) of bivariate relationship (x,y)

Usage

getDensity(x, y, ...)

Arguments

x	numeric (equal length as y)
y	numeric
...	additional parameters passed to MASS::kde2d

Value

density values

Author(s)

Nicholas Mikolajewicz

Kamil Slowikowski (https://slowkow.com/notes/ggplot2-color-by-density/)

Examples

# get data and compute densities
df.meta <- [e-mail] # so is seurat object
df.meta$density1 <- getDensity(df.meta$nCount_RNA, df.meta$percent.mt, n = 100)

# generate scatter plot with overlayed density values
plt.handle1 <- df.meta %>% ggplot(aes(x = nCount_RNA, y = percent.mt, color = density1)) + geom_point() + theme_miko(legend = T) +
   xlab("UMI/cell") + ylab("Mitochondrial Content (%)") +
   labs(title = paste0("r = ", rho1p, "; rho = ", rho1s)) + scale_color_viridis("Density") +
   theme(legend.position="bottom", legend.key.width=unit(legend.width,"cm"))

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.