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plans_integration.R
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plans_integration.R
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## -- Functions to build drake plans for integration analysis.
#' @title Get a `drake` plan for a stage of integration pipeline.
#'
#' @param cfg A list of parameters for this stage
#' (from integration config directory, e.g. loaded from `01_integration.yaml`, etc.).
#' @inheritParams cfg_pipeline_param
#' @param cfg_main A list of general parameters
#' (loaded from `00_main.yaml` from integration config directory).
#'
#' @return [drake::drake_plan()]
#'
#' @concept get_subplan_integration
#' @name get_subplan_integration
NULL
#' @description A plan for 01_integration stage.
#' @rdname get_subplan_integration
#' @export
get_integration_subplan <- function(cfg, cfg_pipeline, cfg_main) {
plan <- drake::drake_plan(
## -- Save config.
config_integration = !!cfg,
## -- Read all single samples from their drake caches.
## -- We cannot easily observe if a particular target from a drake cache has changed,
## -- so we need to always load all sce objects before pipeline run.
## -- Also, some constraints are checked (common normalization method and HVG metrics).
sce_int_import = target(
sce_int_import_fn(!!cfg$INTEGRATION_SOURCES, hvg_combination = !!cfg$HVG_COMBINATION_INT),
trigger = trigger(condition = TRUE)
),
## -- Compute fast SNN clustering for each single-sample, used for integration diagnostics.
sce_int_raw_snn_clustering = sce_int_raw_snn_clustering_fn(
sce_int_import,
snn_k = !!cfg$INTEGRATION_SNN_K,
snn_type = !!cfg$INTEGRATION_SNN_TYPE,
snn_clustering_method = !!cfg$INTEGRATION_SNN_CLUSTERING_METHOD,
BPPARAM = ignore(BiocParallel::bpparam())
),
## -- Subset to common colData, and features (rows) and their corresponding metadata (hvg_ids, hvg_metric_fit).
sce_int_processed = sce_int_processed_fn(sce_int_import),
## -- List of sce objects normalized for inter-batch sequencing depth.
## -- This is the final normalization for "uncorrected" integration, that will just be a sce object merged from these ones.
sce_int_multibatchnorm = batchelor::multiBatchNorm(sce_int_processed, BPPARAM = ignore(BiocParallel::bpparam())),
## -- HVGs.
hvg_int_list = hvg_int_list_fn(
sce_int_multibatchnorm,
hvg_combination = !!cfg$HVG_COMBINATION_INT,
hvg_selection_value = !!cfg$HVG_SELECTION_VALUE_INT,
hvg_selection = !!cfg$HVG_SELECTION_INT
),
## -- Without cell-cycle related genes, if requested.
hvg_int = hvg_int_list$hvg_int,
## -- With all genes, could be NULL.
hvg_int_with_cc = hvg_int_list$hvg_int_with_cc,
## -- Load integration parameters.
integration_methods_df = integration_methods_df_fn(!!cfg$INTEGRATION_METHODS, hvg_int, hvg_int_with_cc),
integration_params_df = dplyr::select(integration_methods_df, name, hvg_rm_cc_genes, hvg_int, integration_params),
## -- Perform the integrations.
sce_int_df = target(
sce_int_df_fn(sce_int_multibatchnorm, integration_params_df, BPPARAM = ignore(BiocParallel::bpparam())),
dynamic = map(integration_params_df)
),
## -- Save uncorrected sce separately.
## -- This tibble will have one or two rows, based on parameter for removal of CC related genes.
sce_int_uncorrected_df = dplyr::filter(sce_int_df, name == "uncorrected"),
gene_annotation = rowData(sce_int_uncorrected_df[1, ]$sce_int[[1]])[, c("ENSEMBL", "SYMBOL", "ENTREZID", "GENENAME")],
single_samples_df = metadata(sce_int_uncorrected_df$sce_int[[1]])$single_samples_df,
hvg_plots_int_df = dplyr::mutate(sce_int_uncorrected_df, hvg_plot = lapply(sce_int, hvg_plot_int_fn)) %>%
dplyr::select(-integration_params, -sce_int),
common_features_count = nrow(sce_int_uncorrected_df$sce_int[[1]]),
## -- Compute PCA for all integration methods.
pca_params_df = dplyr::select(sce_int_df, name, hvg_rm_cc_genes, sce_int) %>%
dplyr::left_join(
dplyr::select(integration_methods_df, name, hvg_rm_cc_genes, pca_selection_method, pca_forced_pcs),
by = c("name", "hvg_rm_cc_genes")
),
sce_int_pca_df = target(
sce_int_pca_df_fn(pca_params_df, BPPARAM = ignore(BiocParallel::bpparam())),
dynamic = map(pca_params_df)
),
sce_int_pca_df_for_report = dplyr::select(sce_int_pca_df, -sce_pca),
## -- MNN clustering for integration diagnostics.
sce_int_clustering_df = target(
sce_int_clustering_df_fn(
sce_int_pca_df,
snn_k = !!cfg$INTEGRATION_SNN_K,
snn_type = !!cfg$INTEGRATION_SNN_TYPE,
snn_clustering_method = !!cfg$INTEGRATION_SNN_CLUSTERING_METHOD,
BPPARAM = ignore(BiocParallel::bpparam())
),
dynamic = map(sce_int_pca_df)
),
int_diagnostics_df = target(
int_diagnostics_df_fn(sce_int_clustering_df, sce_int_raw_snn_clustering),
dynamic = map(sce_int_clustering_df)
),
## -- Compute t-SNE and UMAP.
dimred_params_df = dplyr::select(sce_int_pca_df, name, hvg_rm_cc_genes, sce_pca) %>%
dplyr::left_join(
dplyr::select(integration_methods_df, name, hvg_rm_cc_genes, tsne_perp, tsne_max_iter),
by = c("name", "hvg_rm_cc_genes")
),
sce_int_dimred_df = target(
sce_int_dimred_df_fn(dimred_params_df, BPPARAM = ignore(BiocParallel::bpparam())),
dynamic = map(dimred_params_df)
),
## -- Dimred plots colored by batch and CC phase.
dimred_plots_params_df = dplyr::select(sce_int_dimred_df, name, hvg_rm_cc_genes, sce_dimred) %>%
tidyr::expand_grid(dimred_name = c("pca", "umap", "tsne"), colour_by = c("batch", "phase")) %>%
dplyr::mutate(dimred_name = dplyr::if_else(name == "harmony" & dimred_name == "pca", "harmony", dimred_name)),
sce_int_dimred_plots_df = target(
sce_int_dimred_plots_df_fn(dimred_plots_params_df),
dynamic = map(dimred_plots_params_df)
),
## -- HTML report
report_integration = target(
generate_stage_report(
rmd_file = knitr_in(!!cfg$INTEGRATION_REPORT_RMD_FILE),
out_html_file_name = file_out(!!cfg$INTEGRATION_REPORT_HTML_FILE),
css_file = file_in(!!cfg_main$CSS_FILE),
message = !!cfg$INTEGRATION_KNITR_MESSAGE,
warning = !!cfg$INTEGRATION_KNITR_WARNING,
echo = !!cfg$INTEGRATION_KNITR_ECHO,
other_deps = list(
file_in(!!here("Rmd/common/_header.Rmd")),
file_in(!!here("Rmd/common/_footer.Rmd"))
),
drake_cache_dir = !!cfg_pipeline$DRAKE_CACHE_DIR
),
format = "file"
)
)
## -- Selected markers plots.
if (!is_null(cfg$SELECTED_MARKERS_FILE)) {
plan_selected_markers <- drake::drake_plan(
selected_markers_int_df = selected_markers_int_df_fn(file_in(!!cfg$SELECTED_MARKERS_FILE), sce_int_dimred_df),
selected_markers_int_plots_by = selected_markers_int_df$int_rmcc_dimred,
selected_markers_int_plots_df = target(
selected_markers_int_plots_df_fn(
selected_markers_int_df,
sce_int_dimred_df
),
dynamic = group(selected_markers_int_df, .by = selected_markers_int_plots_by)
),
selected_markers_int_plots_files = target(
save_selected_markers_plots_files(
selected_markers_int_plots_df,
selected_markers_out_dir = !!cfg$INTEGRATION_SELECTED_MARKERS_OUT_DIR,
is_integration = TRUE
),
dynamic = map(selected_markers_int_plots_df)
),
selected_markers_int_plots_files_out = target(
selected_markers_int_plots_files$out_pdf_file,
format = "file"
)
)
} else {
plan_selected_markers <- drake::drake_plan(
selected_markers_int_df = NULL,
selected_markers_int_plots_by = NULL,
selected_markers_int_plots_df = NULL,
selected_markers_int_plots_files = NULL
)
}
return(drake::bind_plans(plan, plan_selected_markers))
}
#' @description A plan for 02_int_clustering stage. The following subplans are included:
#'
#' - [get_clustering_graph_subplan()], [get_clustering_kmeans_subplan()], [get_clustering_sc3_subplan()]
#' - Bound together with [get_clustering_subplan()]
#' - [get_cell_annotation_subplan()]
#' - [get_dimred_plots_other_vars_subplan()]
#' @rdname get_subplan_integration
#' @export
get_int_clustering_subplan <- function(cfg, cfg_pipeline, cfg_main) {
any_clustering_enabled <- any(
cfg$CLUSTER_GRAPH_LOUVAIN_ENABLED, cfg$CLUSTER_GRAPH_WALKTRAP_ENABLED, cfg$CLUSTER_GRAPH_LEIDEN_ENABLED,
cfg$CLUSTER_KMEANS_K_ENABLED, cfg$CLUSTER_KMEANS_KBEST_ENABLED,
cfg$CLUSTER_SC3_ENABLED
)
plan <- drake::drake_plan(
## -- Save config.
config_int_clustering = !!cfg,
sce_int_uncorrected = dplyr::filter(sce_int_uncorrected_df, hvg_rm_cc_genes == !!cfg$INTEGRATION_FINAL_METHOD_RM_CC) %>%
dplyr::pull(sce_int) %>%
.[[1]],
## -- Select the integration method result.
sce_int_final = dplyr::filter(
sce_int_dimred_df,
name == !!cfg$INTEGRATION_FINAL_METHOD,
hvg_rm_cc_genes == !!cfg$INTEGRATION_FINAL_METHOD_RM_CC
) %>%
dplyr::pull(sce_dimred) %>%
.[[1]],
sce_int_final_info = save_object_info(sce_int_final),
additional_cell_data = additional_cell_data_fn(file_in(!!cfg$ADDITIONAL_CELL_DATA_FILE)),
cell_data = cell_data_fn(
col_data = colData(sce_int_final) %>% as.data.frame(),
clusters_all = clusters_all,
cell_annotation_labels = cell_annotation_labels,
cell_groupings = !!cfg$CELL_GROUPINGS,
additional_cell_data = additional_cell_data,
pipeline_type = "integration"
),
sce_int_clustering_final = sce_add_cell_data(sce_int_final, cell_data),
## -- Selected markers plots for the chosen integration method.
selected_markers_int_plots_final = if (is_null(selected_markers_int_plots_files)) {
NULL
} else {
dplyr::filter(
selected_markers_int_plots_files,
name == !!cfg$INTEGRATION_FINAL_METHOD,
hvg_rm_cc_genes == !!cfg$INTEGRATION_FINAL_METHOD_RM_CC
)
},
## -- HTML report
report_int_clustering = target(
generate_stage_report(
rmd_file = knitr_in(!!cfg$INT_CLUSTERING_REPORT_RMD_FILE),
out_html_file_name = file_out(!!cfg$INT_CLUSTERING_REPORT_HTML_FILE),
css_file = file_in(!!cfg_main$CSS_FILE),
message = !!cfg$INT_CLUSTERING_KNITR_MESSAGE,
warning = !!cfg$INT_CLUSTERING_KNITR_WARNING,
echo = !!cfg$INT_CLUSTERING_KNITR_ECHO,
other_deps = list(
file_in(!!here("Rmd/common/_header.Rmd")),
file_in(!!here("Rmd/common/_footer.Rmd")),
file_in(!!fs::dir_ls(here("Rmd/common/clustering"), fail = FALSE))
),
drake_cache_dir = !!cfg_pipeline$DRAKE_CACHE_DIR
),
format = "file"
)
)
if (cfg$INTEGRATION_FINAL_METHOD == "harmony") {
dimred <- "harmony"
} else {
dimred <- "pca"
}
plan_clustering <- get_clustering_subplan(
cfg,
sce_clustering_target_name = "sce_int_final",
sce_dimred_plots_target_name = "sce_int_final",
dimred = dimred,
report_dimred_names = cfg$INT_CLUSTERING_REPORT_DIMRED_NAMES,
dimred_plots_out_dir = cfg$INT_CLUSTERING_DIMRED_PLOTS_OUT_DIR,
other_plots_out_dir = cfg$INT_CLUSTERING_OTHER_PLOTS_OUT_DIR,
is_integration = TRUE,
spatial = FALSE,
seed = cfg_pipeline$SEED
)
plan_cell_annotation <- get_cell_annotation_subplan(
sce_target_name = "sce_int_final",
sce_dimred_plots_target_name = "sce_int_clustering_final",
cell_annotation_sources = cfg$CELL_ANNOTATION_SOURCES,
cell_annotation_out_dir = cfg$INT_CLUSTERING_CELL_ANNOTATION_OUT_DIR,
report_dimred_names = cfg$INT_CLUSTERING_REPORT_DIMRED_NAMES,
dimred_plots_out_dir = cfg$INT_CLUSTERING_DIMRED_PLOTS_OUT_DIR,
do_heatmaps_ = any_clustering_enabled
)
plan_dimred_plots_other_vars <- get_dimred_plots_other_vars_subplan(
sce_target_name = "sce_int_clustering_final",
report_dimred_plots_other = cfg$INT_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER,
report_dimred_names = cfg$INT_CLUSTERING_REPORT_DIMRED_NAMES,
dimred_plots_out_dir = cfg$INT_CLUSTERING_DIMRED_PLOTS_OUT_DIR
)
drake::bind_plans(plan, plan_clustering, plan_cell_annotation, plan_dimred_plots_other_vars)
}