inst/doc/mascarade-gallery.R

In mascarade: Generating Cluster Masks for Single-Cell Dimensional Reduction Plots

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, fig.width = 7, fig.height=5)

## -----------------------------------------------------------------------------
library(mascarade)
library(data.table)
library(ggplot2)
library(ggsci)

## -----------------------------------------------------------------------------
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/pbmc3k_umap.rds"))
data <- data.table(example$dims, 
                   cluster=example$clusters)

maskTable <- generateMask(dims=example$dims, 
                          clusters=example$clusters)

ggplot(data, aes(x=UMAP_1, y=UMAP_2)) + 
    geom_point(aes(color=cluster)) + 
    geom_path(data=maskTable, aes(group=group)) +
    coord_fixed() + 
    theme_classic()
                               

## -----------------------------------------------------------------------------
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/pbmc3k_tsne.rds"))
data <- data.table(example$dims, 
                   cluster=example$clusters)

maskTable <- generateMask(dims=example$dims, 
                          clusters=example$clusters)

ggplot(data, aes(x=tSNE_1, y=tSNE_2)) + 
    geom_point(aes(color=cluster)) + 
    geom_path(data=maskTable, aes(group=group)) +
    coord_fixed() + 
    theme_classic()
                               

## -----------------------------------------------------------------------------
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/aya.rds"))
data <- data.table(example$dims, 
                   cluster=example$clusters)

maskTable <- generateMask(dims=example$dims, 
                          clusters=example$clusters)

ggplot(data, aes(x=UMAP_1, y=UMAP_2)) + 
    geom_point(aes(color=cluster), size=0.5) + 
    geom_path(data=maskTable, aes(group=group)) +
    coord_fixed() + 
    theme_classic()
                               

## -----------------------------------------------------------------------------
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/chiajung1.rds"))
data <- data.table(example$dims, 
                   cluster=example$clusters)

maskTable <- generateMask(dims=example$dims, 
                          clusters=example$clusters)

ggplot(data, aes(x=UMAP_1, y=UMAP_2)) + 
    geom_point(aes(color=cluster), size=0.1) + 
    scale_color_ucscgb() +
    geom_path(data=maskTable, aes(group=group)) +
    coord_fixed() + 
    theme_classic()
                               

## -----------------------------------------------------------------------------
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/chiajung2.rds"))
data <- data.table(example$dims, 
                   cluster=example$clusters)

maskTable <- generateMask(dims=example$dims, 
                          clusters=example$clusters)

ggplot(data, aes(x=UMAP_1, y=UMAP_2)) + 
    geom_point(aes(color=cluster)) + 
    geom_path(data=maskTable, aes(group=group)) +
    coord_fixed() + 
    theme_classic()
                               

## -----------------------------------------------------------------------------
sessionInfo()