integrated_pseudotime.Rmd

# Multi-omic pseudotime

```{r eval=FALSE}

# load coembedding data:
NucSeq.coembed <- readRDS('data/NucSeq_coembed_seurat.rds')
NucSeq_cds <- readRDS('data/NucSeq_coembed_cds.rds')

cur_celltype <- 'MG'

# subset by cell type:
cur_coembed <- NucSeq.coembed %>% subset(Cell.Type == cur_celltype)
cur_cds <- NucSeq_cds[,colnames(cur_coembed)]

cur_cds <- reduce_dimension(cur_cds, reduction_method = 'UMAP', preprocess_method = "Aligned")

# visualize
pdf(paste0('figures/',cur_celltype,'/',cur_celltype,'_monocle_coembedding.pdf'), width=7, height=7)
plot_cells(
  cur_cds,
  color_cells_by = "tech",
  label_cell_groups=FALSE,
  label_leaves=FALSE,
  label_branch_points=FALSE,
  graph_label_size=1.5
)
dev.off()

# move umap from cds to seurat
monocle_umap <- cur_cds@reducedDims[["UMAP"]]
colnames(monocle_umap) <- c('UMAP_1', 'UMAP_2')
all.equal(rownames(monocle_umap), colnames(cur_coembed))
cur_coembed@reductions$umap@cell.embeddings <- monocle_umap
cur_coembed$UMAP_1 <- cur_coembed@reductions[['umap']]@cell.embeddings[,1]
cur_coembed$UMAP_2 <- cur_coembed@reductions[['umap']]@cell.embeddings[,2]

```


Compute pseudotime trajectory on integrated data

```{r eval=FALSE}

# pseudotime with monocle3
cur_cds <- cluster_cells(cur_cds, reduction_method='UMAP')
print(length(unique(partitions(cur_cds))))
cur_cds <- learn_graph(cur_cds)

pdf(paste0("figures/", cur_celltype, "/", cur_celltype, "_coembed_monocle_trajectory_default_pseudotime.pdf"), width=7, height=6)
for(j in 1:length(unique(partitions(cur_cds)))){
  print(j)
  cur_cds = order_cells(
    cur_cds,
    root_pr_nodes = get_earliest_principal_node(
      cur_cds,
      partition = j
    )
  )
  p <- plot_cells(
    cur_cds,
    color_cells_by = "pseudotime",
    label_cell_groups=FALSE,
    label_leaves=FALSE,
    label_branch_points=FALSE,
    graph_label_size=1.5
  )
  print(p)
}
dev.off()

# save seurat obj and cds
saveRDS(cur_coembed, file=paste0('data/',cur_celltype,'_seurat_coembed.rds'))
saveRDS(cur_cds, file=paste0('data/',cur_celltype,'_cds_coembed.rds'))

```