3D visualization of STitch3D’s result on the DLPFC dataset

rm(list = ls())
options(warn=-1)
library(rgl)
library(misc3d)
knitr::knit_hooks$set(webgl = hook_webgl)

Load plot3D functions.

source("./plot3D_func.R")

STitch3D’s spatial domain detection result reveals layer structures in DLPFC.

directory = "./results_DLPFC"
file_list <- list.files(path = directory)
n_slice <- sum(unlist(lapply(file_list, function(x){startsWith(x, "prop_slice")})))

#spatial domains
cluster <- read.table(paste0(directory, "/clustering_result.csv"), sep=",", header=TRUE)
colnames(cluster)[1] <- "spot"

#cell-type proportions
for (i in (0:(n_slice-1))){
    prop <- read.table(paste0(directory, "/prop_slice", i, ".csv"), sep=",", header=TRUE)
    if (i == 0){
        prop_all <- prop
    }else{
        prop_all <- rbind(prop_all, prop)
    }
}
colnames(prop_all)[1] <- "spot"

#3D coordinates
coor_3d <- read.table(paste0(directory, "/3D_coordinates.csv"), sep=",", header=TRUE)
colnames(coor_3d)[1] <- "spot"
spots.table <- merge(coor_3d, prop_all, by=c("spot"))
spots.table <- merge(spots.table, cluster, by=c("spot"))
spots.table$x = -spots.table$x
spots.table$z = (spots.table$z - (spots.table$z > 14) * 397.3) * 200
spots.table$x = spots.table$x / 1.37
spots.table$y = spots.table$y / 1.37
spots.table$z = spots.table$z / 1.37

color = c('#575d6d','#a59c74','#fee838','#00224e','#7d7c78','#d2c060','#2a3f6d')

open3d(windowRect = c(0, 0, 720, 720))

## glX 
##   1

par3d(persp)

## NULL

um <- c(-0.99877554, 0.03325806, 0.0366205, 0,
        0.01137521, -0.56603873, 0.8243002, 0,
        0.04814347, 0.82370752, 0.5649671, 0,
        0.0000000, 0.0000000, 0.0000000, 1) #set the initial view of the 3D plot
view3d(userMatrix = matrix(um, byrow=TRUE, nrow=4))
spheres3d(spots.table$x, spots.table$y, spots.table$z, col = color[spots.table$GM+1], radius=60)
box3d()
axis3d("x-+")
axis3d("y-+")
axis3d("z-+", at=c(0, 2000, 4000, 6000), labels=c(0.0, 10, 310, 320))
title3d(xlab = "x", ylab = "y")
mtext3d("z", "z-+", line = 4)

ct = "Ex_8_L5_6"

open3d(windowRect = c(0, 0, 720, 720))

## glX 
##   3

par3d(persp)

## NULL

um <- c(-0.99877554, 0.03325806, 0.0366205, 0,
        0.01137521, -0.56603873, 0.8243002, 0,
        0.04814347, 0.82370752, 0.5649671, 0,
        0.0000000, 0.0000000, 0.0000000, 1) #set the initial view of the 3D plot
view3d(userMatrix = matrix(um, byrow=TRUE, nrow=4))
spots.table$color <- "gray"
spots.table$color[spots.table[, ct] > 0.2] <- "purple"
spots.table$alpha <- spots.table[, ct]
spots.table$alpha[spots.table[, ct] <= 0.2] <- 0.02
spheres3d(spots.table$x, spots.table$y, spots.table$z, col = spots.table$color, radius=100, alpha=spots.table$alpha)
box3d()
axis3d("x-+")
axis3d("y-+")
axis3d("z-+", at=c(0, 2000, 4000, 6000), labels=c(0.0, 10, 310, 320))
title3d(xlab = "x", ylab = "y")
mtext3d("z", "z-+", line = 4)