3D visualization of STitch3D’s constructed embryo salivary gland

drosophila_embryo_salivary_gland.knit

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 reconstructs the embryo salivary gland.

celltypes <- c("salivary.gland")
celltype_colors <- c("#7f7f7f")
um <- c(0.9776033, -0.2083614, 0.02960751, 0,
        -0.1809667, -0.9040827, -0.38715008, 0,
        0.1074345, 0.3731217, -0.92154104, 0,
        0, 0, 0, 1) #set the initial view of the 3D plot
spot_radius <- 0.5
axis_rescale <- c(1, 1, 1.5)
alpha_threshold <- 0.5
alpha_background <- 0.02

plot3D_proportions(directory = "./results_Drosophila_embryo",
                   celltypes = celltypes,
                   celltype_colors = celltype_colors,
                   um = um,
                   spot_radius = spot_radius,
                   alpha_threshold = alpha_threshold,
                   alpha_background = alpha_background
                   )