## ----echo = FALSE-------------------------------------------------------------
library(knitr)

## ----warning=F, message=F-----------------------------------------------------
library(tradeSeq)
library(RColorBrewer)
library(SingleCellExperiment)

# For reproducibility
palette(brewer.pal(8, "Dark2"))
data(countMatrix, package = "tradeSeq")
counts <- as.matrix(countMatrix)
rm(countMatrix)
data(celltype, package = "tradeSeq")

## ----eval = FALSE-------------------------------------------------------------
# set.seed(22)
# library(monocle3)
# # Create a cell_data_set object
# cds <- new_cell_data_set(counts, cell_metadata = pd,
#                 gene_metadata = data.frame(gene_short_name = rownames(counts),
#                                            row.names = rownames(counts)))
# # Run PCA then UMAP on the data
# cds <- preprocess_cds(cds, method = "PCA")
# cds <- reduce_dimension(cds, preprocess_method = "PCA",
#                         reduction_method = "UMAP")
# 
# # First display, coloring by the cell types from Paul et al
# plot_cells(cds, label_groups_by_cluster = FALSE, cell_size = 1,
#            color_cells_by = "cellType")
# 
# # Running the clustering method. This is necessary to the construct the graph
# cds <- cluster_cells(cds, reduction_method = "UMAP")
# # Visualize the clusters
# plot_cells(cds, color_cells_by = "cluster", cell_size = 1)
# 
# # Construct the graph
# # Note that, for the rest of the code to run, the graph should be fully connected
# cds <- learn_graph(cds, use_partition = FALSE)
# 
# # We find all the cells that are close to the starting point
# cell_ids <- colnames(cds)[pd$cellType ==  "Multipotent progenitors"]
# closest_vertex <- cds@principal_graph_aux[["UMAP"]]$pr_graph_cell_proj_closest_vertex
# closest_vertex <- as.matrix(closest_vertex[colnames(cds), ])
# closest_vertex <- closest_vertex[cell_ids, ]
# closest_vertex <- as.numeric(names(which.max(table(closest_vertex))))
# mst <- principal_graph(cds)$UMAP
# root_pr_nodes <- igraph::V(mst)$name[closest_vertex]
# 
# # We compute the trajectory
# cds <- order_cells(cds, root_pr_nodes = root_pr_nodes)
# plot_cells(cds, color_cells_by = "pseudotime")

## ----eval = FALSE-------------------------------------------------------------
# library(magrittr)
# # Get the closest vertice for every cell
# y_to_cells <-  principal_graph_aux(cds)$UMAP$pr_graph_cell_proj_closest_vertex %>%
#   as.data.frame()
# y_to_cells$cells <- rownames(y_to_cells)
# y_to_cells$Y <- y_to_cells$V1
# 
# # Get the root vertices
# # It is the same node as above
# root <- cds@principal_graph_aux$UMAP$root_pr_nodes
# 
# # Get the other endpoints
# endpoints <- names(which(igraph::degree(mst) == 1))
# endpoints <- endpoints[!endpoints %in% root]
# 
# # For each endpoint
# cellWeights <- lapply(endpoints, function(endpoint) {
#   # We find the path between the endpoint and the root
#   path <- igraph::shortest_paths(mst, root, endpoint)$vpath[[1]]
#   path <- as.character(path)
#   # We find the cells that map along that path
#   df <- y_to_cells[y_to_cells$Y %in% path, ]
#   df <- data.frame(weights = as.numeric(colnames(cds) %in% df$cells))
#   colnames(df) <- endpoint
#   return(df)
#   }) %>% do.call(what = 'cbind', args = .) %>%
#     as.matrix()
# rownames(cellWeights) <- colnames(cds)
# pseudotime <- matrix(pseudotime(cds), ncol = ncol(cellWeights),
#                      nrow = ncol(cds), byrow = FALSE)

## ----eval = FALSE-------------------------------------------------------------
# sce <- fitGAM(counts = counts,
#               pseudotime = pseudotime,
#               cellWeights = cellWeights)

## -----------------------------------------------------------------------------
sessionInfo()