3D visualization of STitch3D’s identified forgut, proventriculus, midgut and hindgut in the Drosophila embryo

drosophila_embryo_guts.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 identifies forgut, proventriculus, midgut and hindgut in the Drosophila embryo.

celltypes <- c("foregut", "hindgut", "midgut", "proventriculus")
celltype_colors <- c("#98df8a", "#d62728", "#9467bd", "#f7b6d2")
um <- c(0.990102768, -0.1285097, 0.0564082, 0,
        -0.140251085, -0.9206678, 0.3642811, 0,
        0.005119142, -0.3685868, -0.9295793, 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
                   )