biopipen 0.32.3__py3-none-any.whl → 0.33.0__py3-none-any.whl

biopipen/scripts/scrna/SeuratClusterStats-clustree.R

@@ -1,15 +1,16 @@
 # srtobj, clustrees_defaults, clustrees
-log_info("clustrees:")
+
+log$info("clustrees:")
+
 if (
     (is.null(clustrees) || length(clustrees) == 0) &&
-    (is.null(clustrees_defaults$prefix) || clustrees_defaults$prefix == "")) {
-    log_warn("- no cases, skipping intentionally ...")
+    (is.null(clustrees_defaults$prefix) || isFALSE(clustrees_defaults$prefix))) {
+    log$warn("- no case specified, skipping ...")
 } else {  # clustrees set or prefix is not empty
-    library(clustree)
     odir = file.path(outdir, "clustrees")
     dir.create(odir, recursive=TRUE, showWarnings=FALSE)
 
-    if ((is.null(clustrees) || length(clustrees) == 0) && clustrees_defaults$prefix == "_auto") {
+    if ((is.null(clustrees) || length(clustrees) == 0) && isTRUE(clustrees_defaults$prefix)) {
         clustrees <- list()
         for (key in names(srtobj@commands)) {
             if (startsWith(key, "FindClusters") && length(srtobj@commands[[key]]$resolution) > 1) {
@@ -23,40 +24,24 @@ if (
         }
     }
     if (length(clustrees) == 0) {
-        log_warn("- no cases found, skipping ...")
+        log$warn("- no case found, skipping ...")
     } else {
         reports <- list()
         for (name in names(clustrees)) {
             if (is.null(clustrees[[name]]$prefix)) {
                 stop(paste0("clustrees: prefix is required for case: ", name))
             }
+            log$info("- Case: {name} ...")
             case <- list_update(clustrees_defaults, clustrees[[name]])
+            extract_vars(case, "devpars", "more_formats", "save_code")
 
-            devpars <- case$devpars
-            devpars$width <- devpars$width %||% clustrees_defaults$devpars$width %||% 800
-            devpars$height <- devpars$height %||% clustrees_defaults$devpars$height %||% 1000
-            devpars$res <- devpars$res %||% clustrees_defaults$devpars$res %||% 100
-            case$devpars <- NULL
             prefix <- sub("\\.$", "", case$prefix)
-            log_info("- Case: {name} ...")
             case$prefix <- paste0(prefix, ".")
-            case$x <- srtobj@meta.data %>% select(starts_with(case$prefix))
-            case$x <- case$x[complete.cases(case$x), , drop = FALSE]
+            case$object <- srtobj
 
             command <- srtobj@commands[[paste0("FindClusters.", prefix)]] %||%
                 (if(prefix == "seurat_clusters") srtobj@commands$FindClusters else NULL)
 
-            p <- do_call(clustree, case)
-            clustree_file <- file.path(odir, paste0(prefix, ".clustree.png"))
-            png(clustree_file, width = devpars$width, height = devpars$height, res = devpars$res)
-            print(p)
-            dev.off()
-
-            clustree_file_pdf <- file.path(odir, paste0(prefix, ".clustree.pdf"))
-            pdf(clustree_file_pdf, width = devpars$width / devpars$res, height = devpars$height / devpars$res)
-            print(p)
-            dev.off()
-
             if (is.null(command)) {
                 resolution <- substring(colnames(case$x), nchar(case$prefix) + 1)
             } else {
@@ -64,16 +49,23 @@ if (
             }
             resolution_used <- resolution[length(resolution)]
 
-            reports[[length(reports) + 1]] <- list(
-                kind = "table_image",
-                src = clustree_file,
-                download = clustree_file_pdf,
-                name = name,
+            plot_prefix <- file.path(odir, paste0(slugify(prefix), ".clustree"))
+            p <- do_call(gglogger::register(ClustreePlot), case)
+            save_plot(p, plot_prefix, devpars, formats = c("png", more_formats))
+
+            if (save_code) {
+                save_plotcode(p, plot_prefix,
+                    setup = c("library(scplotter)", "load('data.RData')", "invisible(list2env('case'))"),
+                    "case",
+                    auto_data_setup = FALSE)
+            }
+            reports[[length(reports) + 1]] <- reporter$image(
+                plot_prefix, more_formats, save_code, kind = "image",
                 descr = paste0("Resolutions: ", paste(resolution, collapse = ", "), "; resolution used: ", resolution_used)
             )
         }
         reports$h1 <- "Clustree plots"
         reports$ui <- "table_of_images"
-        do.call(add_report, reports)
+        do_call(reporter$add, reports)
     }
 }

biopipen/scripts/scrna/SeuratClusterStats-dimplots.R

@@ -2,75 +2,47 @@
 
 # dimplots_defaults = {{envs.dimplots_defaults | r: todot="-"}}
 # dimplots = {{envs.dimplots | r: todot="-", skip=1}}
-log_info("dimplots:")
+log$info("dimplots:")
 
-odir = file.path(outdir, "dimplots")
+odir <- file.path(outdir, "dimplots")
 dir.create(odir, recursive=TRUE, showWarnings=FALSE)
 
 do_one_dimplot = function(name) {
-    log_info("- Case: {name}")
+    log$info("- Case: {name}")
 
-    case = list_update(dimplots_defaults, dimplots[[name]])
-    case$devpars = list_update(dimplots_defaults$devpars, dimplots[[name]]$devpars)
-    if (!is.null(case$subset)) {
-        case$object = srtobj %>% filter(!!rlang::parse_expr(case$subset))
+    case <- list_update(dimplots_defaults, dimplots[[name]])
+
+    # Get functional arguments and inconsistent arguments
+    subset <- case$subset; case$subset <- NULL
+    reduction <- case$reduction; case$reduction <- NULL
+    devpars <- case$devpars; case$devpars <- NULL
+
+    # Normalize arguments
+    reduction <- if (reduction %in% c("dim", "auto")) DefaultDimReduc(srtobj) else reduction
+    devpars <- list_update(dimplots_defaults$devpars, devpars)
+    key <- paste0("sub_umap_", case$group_by)
+
+    if (!is.null(subset)) {
+        case$object <- srtobj %>% filter(!!parse_expr(subset))
     } else {
-        case$object = srtobj
+        case$object <- srtobj
     }
-
-    if (is.null(case$group.by)) { case$group.by = case$ident }
-    key <- paste0("sub_umap_", case$ident)
-    if (
-        key %in% names(case$object@reductions) &&
-        (is.null(case$reduction) || case$reduction %in% c("dim", "auto"))) {
+    if (key %in% names(case$object@reductions) && is.null(reduction)) {
         case$reduction = key
+    } else {
+        case$reduction = reduction
     }
-    if (is.null(case$na_group)) {
-        case$object = filter(case$object, !is.na(!!sym(case$group.by)))
-    } else if (is.null(case$order)) {
-        case$order = case$object@meta.data[[case$group.by]] %>%
-            unique() %>% na.omit() %>% as.character() %>% sort()
-        case$object@meta.data = replace_na(
-            case$object@meta.data,
-            setNames(list(case$na_group), case$group.by)
-        )
-    }
-    case$cols = case$cols %||% pal_biopipen()(length(unique(case$object@meta.data[[case$group.by]])))
-    if (!is.null(case$na_group)) {
-        # Is the NA value in the first position?
-        case$cols = c("lightgrey", case$cols[1:(length(case$cols) - 1)])
-    }
-
-    excluded_args = c("devpars", "ident", "subset")
-    for (arg in excluded_args) {
-        assign(arg, case[[arg]])
-        case[[arg]] = NULL
-    }
-
-    if (case$reduction %in% c("dim", "auto")) { case$reduction = NULL }
-    case$na_group <- NULL
 
-    p = do_call(DimPlot, case)
-    figfile = file.path(odir, paste0(slugify(name), ".dim.png"))
-    png(figfile, width=devpars$width, height=devpars$height, res=devpars$res)
-    print(p)
-    dev.off()
+    p <- do_call(CellDimPlot, case)
+    prefix <- file.path(odir, paste0(slugify(name), ".dim"))
+    save_plot(p, prefix, devpars)
 
-    figfile_pdf = file.path(odir, paste0(slugify(name), ".dim.pdf"))
-    pdf(figfile_pdf, width=devpars$width / devpars$res, height=devpars$height / devpars$res)
-    print(p)
-    dev.off()
-
-    add_report(
+    reporter$add(
         list(
             kind = "descr",
             content = paste0("Dimensionality reduction plot for ", case$group.by)
         ),
-        list(
-            kind = "image",
-            src = figfile,
-            download = figfile_pdf
-        ),
+        reporter$image(prefix, "pdf", FALSE),
         h1 = name
     )
 }