In gofflab/astRal: Spatial Projection Analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(astRal)
library(cocoframer)
library(purrr)
library(viridisLite) # optional - nice color palettes
library(dplyr)
library(reshape2)
library(Seurat)
library(rgl)
library(nat)
#library(sf)
#library(NNLM)

#Sagittal Energy Matrix
ccf_v3_coords_file<-system.file("extdata","p56coord_dev_v3_left.RData",package="astRal")
struct_file<-system.file("extdata","p56_dev_structureID_left.RData",package="astRal")
group_file<-system.file("extdata","group.RData",package="astRal")
energy_file<-system.file("extdata","energy_dev_v3_sagittal.RData",package="astRal")
load(ccf_v3_coords_file)
load(struct_file)
load(group_file)
load(energy_file)

# Get structure ontology annotations
#ga <- get_ccf_grid_annotation()

ontology <- get_mba_ontology()
ontology_df <- flatten_mba_ontology(ontology)

full_ccf_annot<-ccf_annotation(age="Adult",
                               make_array=FALSE,
                               array_spacing=200,
                               coco_reflect=TRUE)

#energy_mat_dims<-aba_array_dims(resolution=200)

# Add column names to energy matrix
colnames(energy.mat)<-rownames(full_ccf_annot)

# Reduce full annotation to only that subset with signal in Allen in situ database
energy.annot<-energy.mat[,coordID_annotation_dev_v3_left]
reduced.annot<-full_ccf_annot[coordID_annotation_dev_v3_left,]

# build a 3d array of ontology structure acronyms - easier to deal with than IDs
#oa <- array(ontology_df$acronym[match(ga, ontology_df$id)], dim = dim(ga))

Create SpatialExperiment object from Allen in situ dataset

se <- NewSpatialExperiment(expression_data=energy.annot,
                           spatial_coords=reduced.annot,
                              barcode_metadata = NULL,
                              gene_metadata = NULL)

spatial_plot_3d(se,color_by="Satb2")

NNMF Patterns

## NNMF100
#energy.lognorm<-LogNormalize(exprs(se))%>%as.matrix()

# Import existing NNMF120 patterns
#patterns_file <- system.file("extdata","NNMF120.1.RData",package="astRal")
load("inst/extdata/NNMF120.1.RData")
pWeights<-NNMF120.1$H
colnames(pWeights)<-rownames(pData(se))
rownames(pWeights)<-paste("pattern",c(1:120),sep="_")
patterns.se<-NewSpatialExperiment(expression_data=pWeights,
                           spatial_coords=reduced.annot,
                              barcode_metadata = NULL,
                              gene_metadata = NULL)

open3d()

par3d(windowRect = c(20, 30, 1200, 1200))

n<-20
start<-81

mat <- matrix(1:n,nrow=4)

layout3d(mat, sharedMouse = TRUE)

xlim<-c(1,max(sf::st_bbox(patterns.se@spatialMap)))
  ylim<-xlim
  zlim<-ylim

for (i in c(start:(start+n))) {

    next3d()

    plot3d(sf::st_coordinates(patterns.se@spatialMap),col=myColorRamp(palette=inferno(100),NNMF120.1$H[i,]),size=3,box=F,axes=F,xlab="",ylab="",zlab="",xlim=xlim,ylim=ylim,zlim=zlim, main=i, alpha=(NNMF120.1$H[i,]-min(NNMF120.1$H[i,]))/(max(NNMF120.1$H[i,])-min(NNMF120.1$H[i,])))
}

i<-88    #67,70,77,101,88,105,106
open3d()
par3d(windowRect = c(20, 30, 1200, 1200))
plot3d(sf::st_coordinates(patterns.se@spatialMap),col=myColorRamp(palette=inferno(100),NNMF120.1$H[i,]),size=10,box=T,axes=T,xlab="",ylab="",zlab="",xlim=xlim,ylim=ylim,zlim=zlim, alpha=(NNMF120.1$H[i,]-min(NNMF120.1$H[i,]))/(max(NNMF120.1$H[i,])-min(NNMF120.1$H[i,])))
movie3d(spin3d(axis = c(1, 1, 1), rpm = 6),duration = 10,movie = paste0("NNMF120",".1","Pattern_", as.character(i)),dir = "/Users/loyalgoff/Downloads/", convert= NULL)
while (rgl.cur() > 0) {
            rgl.close()
      }

open3d()
i<-65 # Look at 69 next and then 75, then 95+CTX
structures <- c("root","RSP")
mesh_list <- map(structures, ccf_2017_mesh)

names(mesh_list) <- structures

xlim<-c(1,max(sf::st_bbox(patterns.se@spatialMap)))
ylim<-xlim
zlim<-ylim

plot_ccf_meshes(mesh_list,
                fg_structure = c("RSP"),
                fg_alpha = 0.2,
                bg_structure = "root",
                style="matte"
                )
par3d(windowRect = c(20, 30, 800, 800))
points3d(sf::st_coordinates(patterns.se@spatialMap),col=myColorRamp(palette=inferno(100),NNMF120.1$H[i,]),size=10,box=T,axes=T,xlab="",ylab="",zlab="", alpha=(NNMF120.1$H[i,]-min(NNMF120.1$H[i,]))/(max(NNMF120.1$H[i,])-min(NNMF120.1$H[i,])))

movie3d(spin3d(axis = c(1, 1, 1), rpm = 12),fps=20, duration = 5,movie = paste0("NNMF120",".1","Pattern_", as.character(i)),dir = "/Users/loyalgoff/Downloads/", convert= NULL)