tests/test_manual.R

In quadbiolab/VoxHunt: Projecting single-cell transcriptomes to spatial brain maps

library(testthat)
library(tidyverse)
library(patchwork)
library(voxhunt)
library(Seurat)

data('example_seurat')
data('brainspan')
data('voxel_meta')
load_aba_data('../voxhunt_data/')
plot_expression('E13', 'NEUROD6')
plot_expression('E15', 'NEUROD6', view='sagittal')

ge_colors <- c('#9fa8da','#8e24aa', '#4a148c', 'lightgray', 'lightgray')
names(ge_colors) <- c('CGE', 'MGE', 'LGE', 'other')
voxhunt::plot_annotation('E13', annotation_level='ge_annot', annotation_colors=ge_colors, alpha=0.1)
ctx_colors <- c('#f8bbd0','#ec407a', '#c2185b', '#880e4f', 'lightgray')
names(ctx_colors) <- c('NPC', 'IP', 'Neuron', 'Neuron2', 'other')
voxhunt::plot_annotation('E18', annotation_level='ctx_annot', annotation_colors=ctx_colors, alpha=0.4, show_legend=T)

markers <- structure_markers('E13')
top10 <- markers %>%
    group_by(group) %>%
    top_n(10, auc) %>%
    {unique(.$gene)}

pb_voxmap <- voxel_map(example_seurat, 'E13', genes_use = top10, pseudobulk_groups = T, group_name = 'cluster')
group_assign <- assign_to_structure(pb_voxmap)
plot_map(pb_voxmap, show_legend = T)
plot_map(pb_voxmap, view='slice', show_legend = F)
plot_map(pb_voxmap, view='sagittal', show_legend = F)
plot_map_3d(pb_voxmap)
plot_map_3d(pb_voxmap, annotation_level = 'custom_2', both_hemispheres = F)


voxmap <- voxel_map(example_seurat, 'E13', genes_use = c('NEUROD6', 'DLX2', 'LHX2'), pseudobulk_groups = F)
cell_assign <- assign_to_structure(voxmap)
plot_map(voxmap, groups = example_seurat$cluster)
plot_map(voxmap, groups = example_seurat$cluster, view='slice')
plot_structure_similarity(voxmap, groups = example_seurat$cluster)


### BrainSpan
pb_bsmap <- brainspan_map(example_seurat, genes_use = top10, pseudobulk_groups = T, group_name = 'cluster')
plot_map(pb_bsmap)

bsmap <- brainspan_map(
    example_seurat,
    genes_use = top10,
    group_name = 'cluster',
    pseudobulk_groups = F
)
bsmap <- brainspan_map(example_seurat, genes_use = c('NEUROD6', 'DLX2'))
plot_map(bsmap)
plot_structure_similarity(bsmap)


### La Manno Mousebrain
load_mousebrain_data('/Users/jfleck/data/2020_linnarson_dev_mouse_brain')
pb_mbmap <- mousebrain_map(example_seurat, genes_use = top10, pseudobulk_groups = T, group_name = 'cluster')
plot_structure_similarity(pb_mbmap, cluster=T)
plot_structure_similarity(pb_mbmap, cluster=F)
plot_map(pb_mbmap)

mbmap <- mousebrain_map(example_seurat, genes_use = top10, pseudobulk_groups = F)
plot_structure_similarity(mbmap, groups = example_seurat$cluster, cluster=F)
plot_map(mbmap, groups = example_seurat$cluster)


### General reference mapping
ref_srt <- example_seurat %>%
    FindVariableFeatures() %>% ScaleData() %>% RunPCA() %>% RunUMAP(dims=1:10)
DimPlot(ref_srt, group.by='cluster')

ref_map <- reference_map(example_seurat, ref_srt, group_name='cluster', genes_use=top10)

plot_map(ref_map, show_legend = T)
summarize_groups(ref_map)