biopipen 0.33.1__py3-none-any.whl → 0.34.0__py3-none-any.whl

biopipen/scripts/scrna/SeuratMap2Ref.R

@@ -1,19 +1,12 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-
-library(parallel)
 library(Seurat)
-library(SeuratDisk)
 library(rlang)
-library(dplyr)
-library(tidyr)
-library(ggplot2)
-library(ggprism)
+library(biopipen.utils)
 
 set.seed(8525)
-theme_set(theme_prism())
 
 sobjfile = {{in.sobjfile | r}}
 outfile = {{out.outfile | r}}
+joboutdir = {{job.outdir | r}}
 use = {{envs.use | r}}
 ident = {{envs.ident | r}}
 ref = {{envs.ref | r}}
@@ -25,8 +18,16 @@ skip_if_normalized = {{envs.skip_if_normalized | r}}
 sctransform_args = {{envs.SCTransform | r: todot="-"}}
 normalizedata_args = {{envs.NormalizeData | r: todot="-"}}
 findtransferanchors_args = {{envs.FindTransferAnchors | r: todot="-"}}
-mappingscore_args = {{envs.MappingScore | r: todot="-"}}
 mapquery_args = {{envs.MapQuery | r: todot="-"}}
+cache = {{envs.cache | r}}
+plots = {{envs.plots | r}}
+
+log <- get_logger()
+reporter <- get_reporter()
+
+options(future.globals.maxSize = 8 * 1024 ^ 4)
+options(future.rng.onMisuse="ignore")
+options(Seurat.object.assay.version = "v5")
 
 # See if we have a reference
 if (is.null(ref)) {
@@ -37,376 +38,74 @@ if (is.null(use)) {
     stop("No use provided (envs.use), don't know which column to transfer as cluster")
 }
 
-if (is.null(mapquery_args$refdata) || length(mapquery_args$refdata) == 0) {
-    mapquery_args$refdata = list()
-}
-
-mapquery_args$refdata[[use]] = use
-
 outdir = dirname(outfile)
+if (isTRUE(cache)) {
+    cache = joboutdir
+}
 if (is.null(split_by)) {
     options(future.globals.maxSize = 8 * 1024 ^ 4)
     future::plan(strategy = "multicore", workers = ncores)
 }
 
-.is_sct <- function(x) {
-    return(Seurat:::IsSCT(assay = x@assays[[DefaultAssay(x)]]))
-}
-
-.expand_dims = function(args, name = "dims") {
-    # Expand dims from 30 to 1:30
-    if (is.numeric(args[[name]]) && length(args[[name]] == 1)) {
-        args[[name]] = 1:args[[name]]
-    }
-    args
-}
-findtransferanchors_args = .expand_dims(findtransferanchors_args)
-
-# Load reference
-log_info("- Loading reference")
-if (endsWith(ref, ".rds") || endsWith(ref, ".RDS")) {
-    reference = readRDS(ref)
-} else if (endsWith(ref, ".h5ad") || endsWith(ref, ".H5AD")) {
-    reference = ReadH5AD(ref)
+log$info("Loading reference ...")
+if (endsWith(ref, ".rds") || endsWith(ref, ".RDS") || endsWith(ref, ".qs") || endsWith(ref, ".qs2")) {
+    reference <- read_obj(ref)
+} else if (endsWith(ref, ".h5seurat") || endsWith(ref, ".H5Seurat")) {
+    reference <- SeuratDisk::LoadH5Seurat(ref)
 } else {
-    reference = LoadH5Seurat(ref)
-}
-reference = UpdateSeuratObject(reference)
-reference = UpdateSCTAssays(reference)
-
-# check if refdata exists in the reference
-for (rname in names(mapquery_args$refdata)) {
-    use_name <- mapquery_args$refdata[[rname]]
-    # transferring an assay
-    if (use_name %in% names(reference)) { next }
-    # transferring a metadata column
-    if (!use_name %in% colnames(reference@meta.data)) {
-        stop(paste0(
-            "The reference does not have the column '",
-            use_name,
-            "' in either assays or metadata. "
-        ))
-        if (startsWith(use_name, "predicted.")) {
-            stop(paste0(
-                "Do you mean: ", substring(use_name, 11),
-            ))
-        }
-    }
-}
-
-if (refnorm == "auto") {
-    refnorm = ifelse (.is_sct(reference), "SCTransform", "NormalizeData")
-}
-if (refnorm == "SCTransform") {
-    # Check if the reference is SCTransform'ed
-    if (!.is_sct(reference)) {
-        stop("Reference is not SCTransform'ed")
-    }
-    n_models = length(x = slot(object = reference[[DefaultAssay(reference)]], name = "SCTModel.list"))
-    if (n_models == 0) {
-        stop("Reference doesn't contain SCTModel.")
-    }
-}
-
-log_info("  Normalization method used: {refnorm}")
-if (refnorm == "SCTransform") {
-    findtransferanchors_args$normalization.method = "SCT"
-} else if (refnorm == "NormalizeData") {
-    findtransferanchors_args$normalization.method = "LogNormalize"
-} else {
-    stop(paste0("Unknown normalization method: ", refnorm))
-}
-
-# Load Seurat object
-log_info("- Loading Seurat object")
-sobj = readRDS(sobjfile)
-defassay <- DefaultAssay(sobj)
-
-if (!is.null(mutaters) && length(mutaters) > 0) {
-    log_info("- Applying mutaters")
-    sobj@meta.data <- sobj@meta.data %>% mutate(!!!lapply(mutaters, parse_expr))
-}
-
-if (!is.null(split_by)) {
-    # check if each split has more than 100 cells
-    cellno = table(sobj@meta.data[[split_by]])
-    cellno = cellno[cellno < 100]
-    if (length(cellno) > 0) {
-        # stop and print the splits with # cells
-        stop(paste0(
-            "The following splits have less than 100 cells: \n",
-            paste0("- ", names(cellno), ": ", cellno, collapse = "\n"),
-            "\n\n",
-            "You can use `envs.mutaters` to merge these splits and use `newsplit` as `envs.split_by`: \n",
-            "> mutaters = {\n",
-            ">   newsplit = \"if_else(oldsplit %in% c('split1', 'split2'), 'mergedsplit', oldsplit)\"\n",
-            "> }\n"
-        ))
-    }
-    sobj = SplitObject(sobj, split.by = split_by)
-}
-
-# Normalize data
-log_info("- Normalizing data")
-if (refnorm == "SCTransform") {
-    if (defassay == "SCT" && skip_if_normalized) {
-        log_warn("  Skipping normalization as the object is already SCTransform'ed")
-    } else {
-        log_info("  Using SCTransform normalization")
-        sctransform_args$residual.features = rownames(x = reference)
-        if (is.null(split_by)) {
-            sctransform_args$object = sobj
-            sobj = do_call(SCTransform, sctransform_args)
-            sctransform_args$object <- NULL
-            rm(sctransform_args)
-            gc()
-        } else {
-            sobj = mclapply(
-                X = sobj,
-                FUN = function(x) {
-                    sctransform_args$object = x
-                    do_call(SCTransform, sctransform_args)
-                },
-                mc.cores = ncores
-            )
-            if (any(unlist(lapply(sobj, class)) == "try-error")) {
-                stop(paste0("\nmclapply (SCTransform) error:", sobj))
-            }
-        }
-    }
-} else {
-    if (defassay == "RNA" && skip_if_normalized) {
-        log_warn("  Skipping normalization as the object is already LogNormalize'd")
-    } else {
-        log_info("  Using NormalizeData normalization")
-        if (is.null(split_by)) {
-            normalizedata_args$object = sobj
-            sobj = do_call(NormalizeData, normalizedata_args)
-        } else {
-            sobj = mclapply(
-                X = sobj,
-                FUN = function(x) {
-                    normalizedata_args$object = x
-                    do_call(NormalizeData, normalizedata_args)
-                },
-                mc.cores = ncores
-            )
-            if (any(unlist(lapply(sobj, class)) == "try-error")) {
-                stop(paste0("\nmclapply (NormalizeData) error:", sobj))
-            }
-        }
-        normalizedata_args$object <- NULL
-        rm(normalizedata_args)
-        gc()
-    }
-}
-
-# Find anchors between query and reference
-log_info("- Finding anchors")
-findtransferanchors_args$reference = reference
-if (is.null(split_by)) {
-    findtransferanchors_args$query = sobj
-    anchors = do_call(FindTransferAnchors, findtransferanchors_args)
-    findtransferanchors_args$reference = NULL
-    findtransferanchors_args$query = NULL
-    rm(findtransferanchors_args)
-    gc()
-} else {
-    anchors = mclapply(
-        X = sobj,
-        FUN = function(x) {
-            findtransferanchors_args$query = x
-            do_call(FindTransferAnchors, findtransferanchors_args)
-        },
-        mc.cores = ncores
-    )
-    if (any(unlist(lapply(anchors, class)) == "try-error")) {
-        stop(paste0("\nmclapply (FindTransferAnchors) error:", anchors))
-    }
-}
-
-# Map query to reference
-log_info("- Mapping query to reference")
-mapquery_args$reference = reference
-if (is.null(split_by)) {
-    mapquery_args$query = sobj
-    mapquery_args$anchorset = anchors
-    sobj = do_call(MapQuery, mapquery_args)
-    mapquery_args$reference = NULL
-    mapquery_args$query = NULL
-    mapquery_args$anchorset = NULL
-    gc()
-} else {
-    sobj = mclapply(
-        X = seq_along(sobj),
-        FUN = function(i) {
-            mapquery_args$query = sobj[[i]]
-            mapquery_args$anchorset = anchors[[i]]
-            do_call(MapQuery, mapquery_args)
-        },
-        mc.cores = ncores
-    )
-    if (any(unlist(lapply(sobj, class)) == "try-error")) {
-        stop(paste0("\nmclapply (MapQuery) error:", sobj))
-    }
-}
-
-# Calculating mapping score
-log_info("- Calculating mapping score")
-mappingscore_sob_msg = paste0(
-    "While calculating mapping score, the following error was encountered: \n",
-    "subscript out of bounds.  \n\n",
-    "You may want to try a smaller `ndim` (default: 50) in `envs.MappingScore`."
-)
-if (is.null(split_by)) {
-    mappingscore_args$anchors = anchors
-    mappingscore = tryCatch({
-        do_call(MappingScore, mappingscore_args)
-    }, error = function(e) {
-        if (e$message == "subscript out of bounds") stop(mappingscore_sob_msg)
-        stop(e)
-    })
-    mappingscore_args$anchors = NULL
-    rm(mappingscore_args)
-    gc()
-} else {
-    mappingscore = mclapply(
-        X = seq_along(sobj),
-        FUN = function(i) {
-            mappingscore_args$anchors = anchors[[i]]
-            tryCatch({
-                do_call(MappingScore, mappingscore_args)
-            }, error = function(e) {
-                if (e$message == "subscript out of bounds") stop(mappingscore_sob_msg)
-                stop(e)
-            })
-        },
-        mc.cores = ncores
-    )
-    if (any(unlist(lapply(mappingscore, class)) == "try-error")) {
-        stop(paste0("\nmclapply (MappingScore) error:", mappingscore))
-    }
-}
-
-# Calculate mapping score and add to metadata
-log_info("- Adding mapping score to metadata")
-if (is.null(split_by)) {
-    sobj = AddMetaData(
-        object = sobj,
-        metadata = mappingscore,
-        col.name = "mapping.score"
-    )
-} else {
-    sobj = mclapply(
-        X = seq_along(sobj),
-        FUN = function(i) {
-            AddMetaData(
-                object = sobj[[i]],
-                metadata = mappingscore[[i]],
-                col.name = "mapping.score"
-            )
-        },
-        mc.cores = ncores
-    )
-    if (any(unlist(lapply(sobj, class)) == "try-error")) {
-        stop(paste0("\nmclapply (AddMetaData) error:", sobj))
-    }
-
-    # Combine the results
-    log_info("- Merging the results")
-    gc()
-    # Memory efficient way to merge the results
-    # query = Reduce(function(x, y) merge(x, y, merge.dr = "ref.umap"), query)
-    sobj = merge(sobj[[1]], sobj[2:length(sobj)], merge.dr = "ref.umap")
-}
-
-# Add the alias to the metadata for the clusters
-log_info("- Adding ident to metadata and set as ident")
-sobj@meta.data = sobj@meta.data %>% mutate(
-    !!sym(ident) := as.factor(!!parse_expr(paste0("predicted.", use)))
+    stop("Reference file must be .qs, .qs2, .rds, .RDS, .h5seurat or .H5Seurat")
+}
+reference <- tryCatch(JoinLayers(reference), error = function(e) {reference})
+Idents(reference) <- reference@meta.data[[use]]
+
+log$info("Loading query data ...")
+sobj <- read_obj(sobjfile)
+
+sobj <- RunSeuratMap2Ref(
+    object = sobj, ref = reference, use = use,
+    ident = ident, refnorm = refnorm, skip_if_normalized = skip_if_normalized,
+    split_by = split_by, ncores = ncores,
+    SCTransformArgs = sctransform_args,
+    NormalizeDataArgs = normalizedata_args,
+    FindTransferAnchorsArgs = findtransferanchors_args,
+    MapQueryArgs = mapquery_args,
+    log = log, cache = cache
 )
-Idents(sobj) = ident
-
-# Check if PrepSCTFindMarkers is done
-if (.is_sct(sobj) && is.null(sobj@commands$PrepSCTFindMarkers)) {
-    log_info("- Running PrepSCTFindMarkers ...")
-    sobj <- PrepSCTFindMarkers(sobj)
-    # compose a new SeuratCommand to record it to sobj@commands
-    commands <- names(pbmc_small@commands)
-    scommand <- pbmc_small@commands[[commands[length(commands)]]]
-    scommand@time.stamp <- Sys.time()
-    scommand@assay.used <- DefaultAssay(sobj)
-    scommand@call.string <- "PrepSCTFindMarkers(object = sobj)"
-    scommand@params <- list()
-    sobj@commands$PrepSCTFindMarkers <- scommand
-}
 
 # Save
-log_info("- Saving result ...")
-saveRDS(sobj, file = outfile)
-
-
-# ############################
-# Some plots
-# ############################
-log_info("- Plotting mapping score ...")
-p <- FeaturePlot(
-    object = sobj,
-    reduction = "ref.umap",
-    features = "mapping.score",
-    cols = c("white", "blue"),
-    pt.size = 0.5
-) + ggtitle("Mapping score for query cells")
-save_plot(p, file.path(outdir, "mapping_score"), list(width = 800, height = 600, res = 100))
+gc()
+log$info("Saving result ...")
+save_obj(sobj, file = outfile)
 
-log_info("- Plotting for transferred data ...")
-ref.reduction = mapquery_args$reduction.model %||% "wnn.umap"
-for (qname in names(mapquery_args$refdata)) {
-    rname <- mapquery_args$refdata[[qname]]
 
-    if (grepl("Array", class(reference[[rname]])) && grepl("Array", class(sobj[[qname]]))) {
-        log_warn("  Skipping transferred array: {qname} -> {rname}")
+### Plotting
+log$info("Plotting features ...")
+for (name in names(plots)) {
+    if (is.null(plots[[name]])) {
         next
     }
-
-    log_info("  UMAP for transferred data: {qname} -> {rname}")
-    ref_p <- DimPlot(
-        object = reference,
-        reduction = ref.reduction,
-        group.by = rname,
-        label = TRUE,
-        label.size = 3,
-        repel = TRUE,
-    ) + NoLegend()
-
-    query_p <- DimPlot(
-        object = sobj,
-        reduction = "ref.umap",
-        group.by = paste0("predicted.", qname),
-        label = TRUE,
-        label.size = 3,
-        repel = TRUE,
-    ) + NoLegend()
-
-    p <- ref_p | query_p
-    prefix <- file.path(outdir, paste0("UMAPs-", slugify(qname)))
-    save_plot(p, prefix, list(width = 1500, height = 700, res = 100))
-
-    # summarize the stats
-    log_info("  Summarizing stats: {qname} -> {rname}")
-    ref_stats <- as.data.frame(table(reference@meta.data[[rname]]))
-    colnames(ref_stats) <- c("CellType", "Count_Ref")
-    query_stats <- as.data.frame(table(sobj@meta.data[[paste0("predicted.", qname)]]))
-    colnames(query_stats) <- c("CellType", "Count_Query")
-    stats <- left_join(ref_stats, query_stats, by = "CellType") %>%
-        replace_na(list(Count_Query = 0)) %>%
-        arrange(desc(Count_Query), desc(Count_Ref))
-
-    write.table(
-        stats,
-        file = file.path(outdir, paste0("stats-", slugify(qname), ".txt")),
-        row.names = FALSE,
-        quote = FALSE,
-        sep = "\t"
+    log$info("- {name} ...")
+    plots[[name]]$features <- gsub("{use}", use, plots[[name]]$features, fixed = TRUE)
+    plots[[name]]$features <- gsub("{ident}", ident, plots[[name]]$features, fixed = TRUE)
+
+    plots[[name]]$devpars <- plots[[name]]$devpars %||% list()
+    plots[[name]]$devpars$res <- plots[[name]]$devpars$res %||% 100
+    plots[[name]]$devpars$width <- plots[[name]]$devpars$width %||% 1200
+    plots[[name]]$devpars$height <- plots[[name]]$devpars$height %||% 720
+    plots[[name]]$more_formats <- plots[[name]]$more_formats %||% character()
+    plots[[name]]$save_code <- FALSE
+    plots[[name]]$descr <- plots[[name]]$descr %||% name
+    extract_vars(plots[[name]], "devpars", "more_formats", "save_code", "descr")
+
+    plot_fn <- gglogger::register(VizSeuratMap2Ref)
+    p <- do_call(plot_fn, c(list(query = sobj, ref = reference), plots[[name]]))
+    prefix <- file.path(outdir, paste0(slugify(name), ".map2ref"))
+    save_plot(p, prefix, devpars, formats = c("png", more_formats))
+
+    reporter$add(
+        reporter$image(prefix, more_formats, save_code = FALSE, kind = "image"),
+        h1 = name
     )
 }
+
+reporter$save(joboutdir)

biopipen/scripts/scrna/SeuratMetadataMutater.R

@@ -1,17 +1,15 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-{{ biopipen_dir | joinpaths: "utils", "mutate_helpers.R" | source_r }}
-
 library(rlang)
 library(tibble)
 library(dplyr)
 library(Seurat)
+library(biopipen.utils)
 
-srtobj = {{in.srtobj | quote}}
+srtobj = {{in.srtobj | r}}
 metafile = {{in.metafile | r}}
 mutaters = {{envs.mutaters | r}}
-rdsfile = {{out.rdsfile | quote}}
+outfile = {{out.outfile | r}}
 
-srt = readRDS(srtobj)
+srt = read_obj(srtobj)
 metadata = srt@meta.data
 
 if (!is.null(metafile)) {
@@ -40,4 +38,4 @@ if (!is.null(expr) && length(expr) > 0) {
     srt@meta.data = metadata
 }
 
-saveRDS(srt, rdsfile)
+save_obj(srt, outfile)

biopipen/scripts/scrna/SeuratPreparing.R

@@ -5,9 +5,9 @@ library(dplyr)
 library(glue)
 library(biopipen.utils)
 
-metafile <- {{in.metafile | quote}}
-rdsfile <- {{out.rdsfile | quote}}
-joboutdir <- {{job.outdir | quote}}
+metafile <- {{in.metafile | r}}
+outfile <- {{out.outfile | r}}
+joboutdir <- {{job.outdir | r}}
 envs <- {{envs | r: todot = "-", skip = 1}}
 
 if (isTRUE(envs$cache)) { envs$cache <- joboutdir }
@@ -30,7 +30,9 @@ reporter$add(
             "<p>Cell filters: ", html_escape(envs$cell_qc), "</p>",
             "<p>Gene filters: </p>",
             "<p>- Min Cells: ", envs$gene_qc$min_cells, "</p>",
-            "<p>- Excludes: ", html_escape(envs$gene_qc$excludes %||% "Not set"), "</p>"
+            "<p>- Excludes: ",
+            ifelse(is.null(envs$gene_qc$excludes), "Not set", paste(envs$gene_qc$excludes, collapse = ", ")),
+            "</p>"
         )
     ),
     h1 = "Filters and QC"
@@ -57,43 +59,77 @@ dir.create(qcdir, showWarnings = FALSE, recursive = TRUE)
 
 sobj <- LoadSeuratAndPerformQC(
     metadata,
-    per_sample_qc = envs$cell_qc_per_sample,
+    min_cells = envs$min_cells,
+    min_features = envs$min_features,
     cell_qc = envs$cell_qc,
     gene_qc = envs$gene_qc,
     tmpdir = joboutdir,
     log = log,
     cache = envs$cache)
 
-log$info("Saving dimension table ...")
-dim_df <- data.frame(
-    when = c("Before QC", "After QC"),
-    nCells = c(nrow(sobj@misc$cell_qc_df), sum(sobj@misc$cell_qc_df$.QC)),
-    nGenes = c(sobj@misc$gene_qc$before, sobj@misc$gene_qc$after)
-)
-write.table(dim_df, file = file.path(qcdir, "dim.txt"),
+log$info("Saving and visualizing QC results ...")
+cell_qc_df <- VizSeuratCellQC(sobj, plot_type = "table")
+write.table(cell_qc_df, file = file.path(qcdir, "cell_qc.txt"),
             row.names = FALSE, quote = FALSE, sep = "\t")
 
 reporter$add(
     list(
-        kind = "descr",
-        content = "The dimension table for the Seurat object. The table contains the number of cells and genes before and after QC. Note that the cell QC is performed before gene QC."
+        name = "Cell QC metrics",
+        contents = list(
+            list(
+                kind = "descr",
+                content = paste0(
+                    "The table below show the number of cells in each sample that failed and passed the QC filters. ",
+                    "The last row shows the total number of cells that failed and passed the QC filters across all samples. "
+                )
+            ),
+            list(kind = "table", src = file.path(qcdir, "cell_qc.txt"))
+        )
     ),
+    h1 = "Filters and QC",
+    h2 = "Cell-level Quality Control",
+    ui = "tabs"
+)
+
+gene_qc_df <- VizSeuratGeneQC(sobj, plot_type = "table")
+write.table(gene_qc_df, file = file.path(qcdir, "gene_qc.txt"),
+            row.names = FALSE, quote = FALSE, sep = "\t")
+
+reporter$add(
     list(
-        kind = "table",
-        data = list(path = file.path(qcdir, "dim.txt"))
+        name = "Gene QC metrics",
+        contents = list(
+            list(
+                kind = "descr",
+                content = paste0(
+                    "The table below show the number of genes in each sample that failed and passed the QC filters. ",
+                    "The last row shows the final number of genes that failed and passed the QC filters across all samples. ",
+                    "Any gene that failed the QC filters will be excluded in the merged Seurat object."
+                )
+            ),
+            list(kind = "table", src = file.path(qcdir, "gene_qc.txt")),
+            list(kind = "list", items = list(paste0(
+                "We may still end up with features slightly less than the final passed ones. ",
+                "For example, when SCTransform is used, the number of features may be less than the number of genes that passed the QC filters. ",
+                "This is because SCTransform selects the top N features based on variance. "
+            )))
+        )
     ),
     h1 = "Filters and QC",
-    h2 = "Dimension table"
+    h2 = "Gene-level Quality Control",
+    ui = "tabs"
 )
 
-log$info("Visualizing QC metrics ...")
 for (pname in names(envs$qc_plots)) {
+    if (is.null(envs$qc_plots[[pname]])) next
+    log$info("- {pname} ...")
     args <- envs$qc_plots[[pname]]
     args$kind <- args$kind %||% "cell"
     args$devpars <- args$devpars %||% list()
     args$more_formats <- args$more_formats %||% character()
     args$save_code <- args$save_code %||% FALSE
-    extract_vars(args, "kind", "devpars", "more_formats", "save_code")
+    args$descr <- args$descr %||% pname
+    extract_vars(args, "kind", "devpars", "more_formats", "save_code", "descr")
     if (kind == "gene") kind <- "gene_qc"
     if (kind == "cell") kind <- "cell_qc"
     args$object <- sobj
@@ -103,21 +139,31 @@ for (pname in names(envs$qc_plots)) {
         gglogger::register(VizSeuratGeneQC)
     }
     p <- do_call(plot_fn, args)
-    prefix <- file.path(qcdir, paste0(slugify(pname), "_", kind))
+    prefix <- file.path(qcdir, paste0(slugify(pname), ".", kind))
     save_plot(p, prefix, devpars, formats = c("png", more_formats))
     if (save_code) {
         save_plotcode(p, prefix,
-            setup = c("library(biopipen.utils)", "load('data.RData')", "invisible(list2env('args'))"),
+            setup = c("library(biopipen.utils)", "load('data.RData')", "invisible(list2env(args, envir = .GlobalEnv))"),
             "args",
             auto_data_setup = FALSE)
     }
     reporter$add(
-        reporter$image(prefix, more_formats, save_code, kind = "image"),
+        list(
+            name = pname,
+            contents = list(
+                list(kind = "descr", content = descr),
+                reporter$image(prefix, more_formats, save_code, kind = "image")
+            )
+        ),
         h1 = "Filters and QC",
-        h2 = html_escape(pname)
+        h2 = ifelse(kind == "cell_qc", "Cell-level Quality Control", "Gene-level Quality Control"),
+        ui = "tabs"
     )
 }
 
+log$info("Filtering with QC criteria ...")
+sobj <- FinishSeuratQC(sobj)
+
 sobj <- RunSeuratTransformation(
     sobj,
     use_sct = envs$use_sct,
@@ -194,6 +240,12 @@ if (!identical(envs$doublet_detector, "none")) {
     sobj <- subset(sobj, subset = !!sym(paste0(sobj@misc$doublets$tool, "_DropletType")) != "doublet")
 }
 
+if (!is.null(envs$mutaters) && length(envs$mutaters) > 0) {
+    log$info("Mutating metadata ...")
+    sobj@meta.data <- sobj@meta.data %>%
+        mutate(!!!lapply(envs$mutaters, rlang::parse_expr))
+}
+
 log$info("Saving QC'ed seurat object ...")
 reporter$save(joboutdir)
-saveRDS(sobj, rdsfile)
+save_obj(sobj, outfile)