biopipen 0.33.1__py3-none-any.whl → 0.34.1__py3-none-any.whl

biopipen/ns/scrna.py

@@ -1,16 +1,17 @@
 """Tools to analyze single-cell RNA"""
 
+from pipen.utils import mark
 from ..core.proc import Proc
 from ..core.config import config
-from ..utils.common_docstrs import (
-    indent_docstr,
-    format_placeholder,
-    MUTATE_HELPERS_CLONESIZE,
-    ENVS_SECTION_EACH,
-)
+# from ..utils.common_docstrs import (
+#     indent_docstr,
+#     format_placeholder,
+#     MUTATE_HELPERS_CLONESIZE,
+#     ENVS_SECTION_EACH,
+# )
 
-MUTATE_HELPERS_CLONESIZE_INDENTED = indent_docstr(MUTATE_HELPERS_CLONESIZE, "    " * 3)
-ENVS_SECTION_EACH_INDENTED = indent_docstr(ENVS_SECTION_EACH, "    " * 3)
+# MUTATE_HELPERS_CLONESIZE_INDENTED = indent_docstr(MUTATE_HELPERS_CLONESIZE, "    " * 3)
+# ENVS_SECTION_EACH_INDENTED = indent_docstr(ENVS_SECTION_EACH, "    " * 3)
 
 
 class SeuratLoading(Proc):
@@ -60,7 +61,8 @@ class SeuratPreparing(Proc):
     Those paths should be either paths to directoies containing `matrix.mtx`,
     `barcodes.tsv` and `features.tsv` files that can be loaded by
     [`Seurat::Read10X()`](https://satijalab.org/seurat/reference/read10x),
-    or paths to `h5` files that can be loaded by
+    or paths of loom files that can be loaded by `SeuratDisk::LoadLoom()`, or paths to
+    `h5` files that can be loaded by
     [`Seurat::Read10X_h5()`](https://satijalab.org/seurat/reference/read10x_h5).
 
     Each sample will be loaded individually and then merged into one `Seurat` object, and then perform QC.
@@ -96,14 +98,24 @@ class SeuratPreparing(Proc):
             to the h5 file that can be read by `Read10X_h5()` from `Seurat`.
 
     Output:
-        rdsfile: The RDS file with the Seurat object with all samples integrated.
+        outfile: The qs2 file with the Seurat object with all samples integrated.
             Note that the cell ids are prefixied with sample names.
-            QC plots will be saved in `<job.outdir>/plots`.
 
     Envs:
         ncores (type=int): Number of cores to use.
             Used in `future::plan(strategy = "multicore", workers = <ncores>)`
             to parallelize some Seurat procedures.
+        mutaters (type=json): The mutaters to mutate the metadata to the cells.
+            These new columns will be added to the metadata of the Seurat object and
+            will be saved in the output file.
+        min_cells (type=int): The minimum number of cells that a gene must be
+            expressed in to be kept. This is used in `Seurat::CreateSeuratObject()`.
+            Futher QC (`envs.cell_qc`, `envs.gene_qc`) will be performed after this.
+            It doesn't work when data is loaded from loom files.
+        min_features (type=int): The minimum number of features that a cell must
+            express to be kept. This is used in `Seurat::CreateSeuratObject()`.
+            Futher QC (`envs.cell_qc`, `envs.gene_qc`) will be performed after this.
+            It doesn't work when data is loaded from loom files.
         cell_qc: Filter expression to filter cells, using
             `tidyrseurat::filter()`.
             Available QC keys include `nFeature_RNA`, `nCount_RNA`,
@@ -122,9 +134,6 @@ class SeuratPreparing(Proc):
             genes.
             ///
 
-        cell_qc_per_sample (flag): Whether to perform cell QC per sample or not.
-            If `True`, the cell QC will be performed per sample, and the QC will be
-            applied to each sample before merging.
         gene_qc (ns): Filter genes.
             `gene_qc` is applied after `cell_qc`.
             - min_cells: The minimum number of cells that a gene must be
@@ -259,34 +268,37 @@ class SeuratPreparing(Proc):
     """  # noqa: E501
 
     input = "metafile:file"
-    output = "rdsfile:file:{{in.metafile | stem}}.seurat.RDS"
+    output = "outfile:file:{{in.metafile | stem}}.seurat.qs"
     lang = config.lang.rscript
+    envs_depth = 4
     envs = {
         "ncores": config.misc.ncores,
+        "mutaters": {},
+        "min_cells": 0,
+        "min_features": 0,
         "cell_qc": None,  # "nFeature_RNA > 200 & percent.mt < 5",
-        "cell_qc_per_sample": False,
         "gene_qc": {"min_cells": 0, "excludes": []},
         "qc_plots": {
-            "Violin Plots of QC Metrics": {
+            "Violin Plots": {
                 "kind": "cell",
                 "plot_type": "violin",
                 "devpars": {"res": 100, "height": 600, "width": 1200},
             },
-            "Scatter Plots of QC Metrics": {
+            "Scatter Plots": {
                 "kind": "cell",
                 "plot_type": "scatter",
                 "devpars": {"res": 100, "height": 800, "width": 1200},
             },
-            "Ridge Plots of QC Metrics": {
+            "Ridge Plots": {
                 "kind": "cell",
                 "plot_type": "ridge",
                 "devpars": {"res": 100, "height": 800, "width": 1200},
             },
-            # "Number of Expressing Cells for Excluded Genes (10)": {
-            #     "kind": "gene",
-            #     "features": 10,
-            #     "devpars": {"res": 100, "height": 1200, "width": 1200}
-            # },
+            "Distribution of number of cells a gene is expressed in": {
+                "kind": "gene",
+                "plot_type": "histogram",
+                "devpars": {"res": 100, "height": 1200, "width": 1200},
+            },
         },
         "use_sct": False,
         "no_integration": False,
@@ -297,6 +309,7 @@ class SeuratPreparing(Proc):
         "SCTransform": {
             "return-only-var-genes": True,
             "min_cells": 5,
+            "verbose": True,
         },
         "IntegrateLayers": {"method": "harmony"},
         "doublet_detector": "none",
@@ -306,7 +319,7 @@ class SeuratPreparing(Proc):
     }
     script = "file://../scripts/scrna/SeuratPreparing.R"
     plugin_opts = {
-        "report": "file://../reports/scrna/SeuratPreparing.svelte",
+        "report": "file://../reports/common.svelte",
     }
 
 
@@ -318,24 +331,13 @@ class SeuratClustering(Proc):
         srtobj: The seurat object loaded by SeuratPreparing
 
     Output:
-        rdsfile: The seurat object with cluster information at `seurat_clusters`
-            If `SCTransform` was used, the default Assay will be reset to `RNA`.
+        outfile: The seurat object with cluster information at `seurat_clusters`.
 
     Envs:
         ncores (type=int;order=-100): Number of cores to use.
             Used in `future::plan(strategy = "multicore", workers = <ncores>)`
             to parallelize some Seurat procedures.
             See also: <https://satijalab.org/seurat/articles/future_vignette.html>
-        ScaleData (ns): Arguments for [`ScaleData()`](https://satijalab.org/seurat/reference/scaledata).
-            If you want to re-scale the data by regressing to some variables, `Seurat::ScaleData`
-            will be called. If nothing is specified, `Seurat::ScaleData` will not be called.
-            - vars-to-regress: The variables to regress on.
-            - <more>: See <https://satijalab.org/seurat/reference/scaledata>
-        SCTransform (ns): Arguments for [`SCTransform()`](https://satijalab.org/seurat/reference/sctransform).
-            If you want to re-scale the data by regressing to some variables, `Seurat::SCTransform`
-            will be called. If nothing is specified, `Seurat::SCTransform` will not be called.
-            - vars-to-regress: The variables to regress on.
-            - <more>: See <https://satijalab.org/seurat/reference/sctransform>
         RunUMAP (ns): Arguments for [`RunUMAP()`](https://satijalab.org/seurat/reference/runumap).
             `object` is specified internally, and `-` in the key will be replaced with `.`.
             `dims=N` will be expanded to `dims=1:N`; The maximal value of `N` will be the minimum of `N` and the number of columns - 1 for each sample.
@@ -343,6 +345,7 @@ class SeuratClustering(Proc):
             - reduction: The reduction to use for UMAP.
                 If not provided, `sobj@misc$integrated_new_reduction` will be used.
             - <more>: See <https://satijalab.org/seurat/reference/runumap>
+        RunPCA (ns): Arguments for [`RunPCA()`](https://satijalab.org/seurat/reference/runpca).
         FindNeighbors (ns): Arguments for [`FindNeighbors()`](https://satijalab.org/seurat/reference/findneighbors).
             `object` is specified internally, and `-` in the key will be replaced with `.`.
             - reduction: The reduction to use.
@@ -357,14 +360,9 @@ class SeuratClustering(Proc):
                 The results will be saved in `seurat_clusters_<resolution>`.
                 The final resolution will be used to define the clusters at `seurat_clusters`.
             - <more>: See <https://satijalab.org/seurat/reference/findclusters>
-        cache (type=auto): Whether to cache the information at different steps.
+        cache (type=auto): Where to cache the information at different steps.
             If `True`, the seurat object will be cached in the job output directory, which will be not cleaned up when job is rerunning.
-            The cached seurat object will be saved as `<signature>.<kind>.RDS` file, where `<signature>` is the signature determined by
-            the input and envs of the process.
-            See <https://github.com/satijalab/seurat/issues/7849>, <https://github.com/satijalab/seurat/issues/5358> and
-            <https://github.com/satijalab/seurat/issues/6748> for more details also about reproducibility issues.
-            To not use the cached seurat object, you can either set `cache` to `False` or delete the cached file at
-            `<signature>.RDS` in the cache directory.
+            Set to `False` to not cache the results.
 
     Requires:
         r-seurat:
@@ -376,13 +374,12 @@ class SeuratClustering(Proc):
     """  # noqa: E501
 
     input = "srtobj:file"
-    output = "rdsfile:file:{{in.srtobj | stem}}.RDS"
+    output = "outfile:file:{{in.srtobj | stem}}.qs"
     lang = config.lang.rscript
     envs = {
         "ncores": config.misc.ncores,
-        "ScaleData": {},
-        "SCTransform": {},
-        "RunUMAP": {"dims": 30},
+        "RunPCA": {},
+        "RunUMAP": {},
         "FindNeighbors": {},
         "FindClusters": {"resolution": 0.8},
         "cache": config.path.tmpdir,
@@ -399,15 +396,15 @@ class SeuratSubClustering(Proc):
 
     For the subset of cells, the reductions will be re-performed on the subset of cells,
     and then the clustering will be performed on the subset of cells. The reduction
-    will be saved in `sobj@reduction$sub_umap_<casename>` of the original object and the
-    clustering will be saved in the metadata of the original object using the casename \
+    will be saved in `object@reduction$<casename>.<reduction>` of the original object and the
+    clustering will be saved in the metadata of the original object using the casename
     as the column name.
 
     Input:
-        srtobj: The seurat object
+        srtobj: The seurat object in RDS or qs/qs2 format.
 
     Output:
-        rdsfile: The seurat object with the subclustering information.
+        outfile: The seurat object with the subclustering information in qs/qs2 format.
 
     Envs:
         ncores (type=int;order=-100): Number of cores to use.
@@ -417,7 +414,9 @@ class SeuratSubClustering(Proc):
             The mutaters will be applied in the order specified.
         subset: An expression to subset the cells, will be passed to
             [`tidyseurat::filter()`](https://stemangiola.github.io/tidyseurat/reference/filter.html).
-
+        RunPCA (ns): Arguments for [`RunPCA()`](https://satijalab.org/seurat/reference/runpca).
+            `object` is specified internally as the subset object, and `-` in the key will be replaced with `.`.
+            - <more>: See <https://satijalab.org/seurat/reference/runpca>
         RunUMAP (ns): Arguments for [`RunUMAP()`](https://satijalab.org/seurat/reference/runumap).
             `object` is specified internally as the subset object, and `-` in the key will be replaced with `.`.
             `dims=N` will be expanded to `dims=1:N`; The maximal value of `N` will be the minimum of `N` and the number of columns - 1 for each sample.
@@ -428,7 +427,7 @@ class SeuratSubClustering(Proc):
         FindNeighbors (ns): Arguments for [`FindNeighbors()`](https://satijalab.org/seurat/reference/findneighbors).
             `object` is specified internally, and `-` in the key will be replaced with `.`.
             - reduction: The reduction to use.
-                If not provided, `sobj@misc$integrated_new_reduction` will be used.
+                If not provided, `object@misc$integrated_new_reduction` will be used.
             - <more>: See <https://satijalab.org/seurat/reference/findneighbors>
         FindClusters (ns): Arguments for [`FindClusters()`](https://satijalab.org/seurat/reference/findclusters).
             `object` is specified internally, and `-` in the key will be replaced with `.`.
@@ -438,32 +437,33 @@ class SeuratSubClustering(Proc):
                 The results will be saved in `<casename>_<resolution>`.
                 The final resolution will be used to define the clusters at `<casename>`.
             - <more>: See <https://satijalab.org/seurat/reference/findclusters>
-        cache (type=auto): Whether to cache the information at different steps.
+        cache (type=auto): Whether to cache the results.
             If `True`, the seurat object will be cached in the job output directory, which will be not cleaned up when job is rerunning.
-            The cached seurat object will be saved as `<signature>.<kind>.RDS` file, where `<signature>` is the signature determined by
-            the input and envs of the process.
-            See <https://github.com/satijalab/seurat/issues/7849>, <https://github.com/satijalab/seurat/issues/5358> and
-            <https://github.com/satijalab/seurat/issues/6748> for more details also about reproducibility issues.
-            To not use the cached seurat object, you can either set `cache` to `False` or delete the cached file at
-            `<signature>.RDS` in the cache directory.
+            Set to `False` to not cache the results.
         cases (type=json): The cases to perform subclustering.
             Keys are the names of the cases and values are the dicts inherited from `envs` except `mutaters` and `cache`.
             If empty, a case with name `subcluster` will be created with default parameters.
+            The case name will be passed to `biopipen.utils::SeuratSubCluster()` as `name`.
+            It will be used as the prefix for the reduction name, keys and cluster names.
+            For reduction keys, it will be `toupper(<name>)` + "PC_" and `toupper(<name>)` + "UMAP_".
+            For cluster names, it will be `<name>` + "." + resolution.
+            And the final cluster name will be `<name>`.
+            Note that the `name` should be alphanumeric and anything other than alphanumeric will be removed.
     """  # noqa: E501
-
     input = "srtobj:file"
-    output = "rdsfile:file:{{in.srtobj | stem}}.RDS"
+    output = "outfile:file:{{in.srtobj | stem}}.qs"
     lang = config.lang.rscript
     envs_depth = 1
     envs = {
         "ncores": config.misc.ncores,
         "mutaters": {},
         "subset": None,
-        "RunUMAP": {"dims": 30},
+        "RunPCA": {},
+        "RunUMAP": {},
         "FindNeighbors": {},
         "FindClusters": {"resolution": 0.8},
         "cache": config.path.tmpdir,
-        "cases": {"subcluster": {}},
+        "cases": {},
     }
     script = "file://../scripts/scrna/SeuratSubClustering.R"
 
@@ -533,12 +533,17 @@ class SeuratClusterStats(Proc):
     Envs:
         mutaters (type=json): The mutaters to mutate the metadata to subset the cells.
             The mutaters will be applied in the order specified.
+        cache (type=auto): Whether to cache the plots.
+            Currently only plots for features are supported, since creating the those
+            plots can be time consuming.
+            If `True`, the plots will be cached in the job output directory, which will
+            be not cleaned up when job is rerunning.
         clustrees_defaults (ns): The parameters for the clustree plots.
             - devpars (ns): The device parameters for the clustree plot.
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
                 - width (type=int): The width of the plots.
-            - more_formats (list): The formats to save the plots other than `png`.
+            - more_formats (type=list): The formats to save the plots other than `png`.
             - save_code (flag): Whether to save the code to reproduce the plot.
             - prefix (type=auto): string indicating columns containing clustering information.
                 The trailing dot is not necessary and will be added automatically.
@@ -561,7 +566,7 @@ class SeuratClusterStats(Proc):
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
                 - width (type=int): The width of the plots.
-            - more_formats (list): The formats to save the plots other than `png`.
+            - more_formats (type=list): The formats to save the plots other than `png`.
             - save_code (flag): Whether to save the code to reproduce the plot.
             - save_data (flag): Whether to save the data used to generate the plot.
             - <more>: Other arguments passed to `scplotter::CellStatPlot`.
@@ -576,10 +581,7 @@ class SeuratClusterStats(Proc):
             >>> }
         ngenes_defaults (ns): The default parameters for `ngenes`.
             The default parameters to plot the number of genes expressed in each cell.
-            - ident: The column name in metadata to use as the identity.
-            - group-by: The column name in metadata to group the cells.
-                Dodge position will be used to separate the groups.
-            - split-by: The column name in metadata to split the cells into different plots.
+            - more_formats (type=list): The formats to save the plots other than `png`.
             - subset: An expression to subset the cells, will be passed to `tidyrseurat::filter()`.
             - devpars (ns): The device parameters for the plots.
                 - res (type=int): The resolution of the plots.
@@ -588,9 +590,11 @@ class SeuratClusterStats(Proc):
         ngenes (type=json): The number of genes expressed in each cell.
             Keys are the names of the plots and values are the dicts inherited from `env.ngenes_defaults`.
         features_defaults (ns): The default parameters for `features`.
-            - features: The features to plot.
+            - features (type=auto): The features to plot.
                 It can be either a string with comma separated features, a list of features, a file path with `file://` prefix with features
                 (one per line), or an integer to use the top N features from `VariantFeatures(srtobj)`.
+                It can also be a dict with the keys as the feature group names and the values as the features, which
+                is used for heatmap to group the features.
             - order_by (type=auto): The order of the clusters to show on the plot.
                 An expression passed to `dplyr::arrange()` on the grouped meta data frame (by `ident`).
                 For example, you can order the clusters by the activation score of
@@ -603,7 +607,7 @@ class SeuratClusterStats(Proc):
                 - height (type=int): The height of the plots.
                 - width (type=int): The width of the plots.
             - descr: The description of the plot, showing in the report.
-            - more_formats (list): The formats to save the plots other than `png`.
+            - more_formats (type=list): The formats to save the plots other than `png`.
             - save_code (flag): Whether to save the code to reproduce the plot.
             - save_data (flag): Whether to save the data used to generate the plot.
             - <more>: Other arguments passed to `scplotter::FeatureStatPlot`.
@@ -643,6 +647,7 @@ class SeuratClusterStats(Proc):
     lang = config.lang.rscript
     envs = {
         "mutaters": {},
+        "cache": config.path.tmpdir,
         "clustrees_defaults": {
             "devpars": {"res": 100},
             "more_formats": [],
@@ -667,10 +672,8 @@ class SeuratClusterStats(Proc):
             },
         },
         "ngenes_defaults": {
-            "ident": "seurat_clusters",
-            "group-by": None,
-            "split-by": None,
             "subset": None,
+            "more_formats": [],
             "devpars": {"res": 100, "height": 800, "width": 1000},
         },
         "ngenes": {
@@ -702,7 +705,10 @@ class SeuratClusterStats(Proc):
         },
     }
     script = "file://../scripts/scrna/SeuratClusterStats.R"
-    plugin_opts = {"report": "file://../reports/scrna/SeuratClusterStats.svelte"}
+    plugin_opts = {
+        "report": "file://../reports/common.svelte",
+        "report_paging": 8,
+    }
 
 
 class ModuleScoreCalculator(Proc):
@@ -781,7 +787,7 @@ class ModuleScoreCalculator(Proc):
     """  # noqa: E501
 
     input = "srtobj:file"
-    output = "rdsfile:file:{{in.srtobj | stem}}.RDS"
+    output = "rdsfile:file:{{in.srtobj | stem}}.qs"
     lang = config.lang.rscript
     envs = {
         "defaults": {
@@ -805,9 +811,11 @@ class ModuleScoreCalculator(Proc):
     script = "file://../scripts/scrna/ModuleScoreCalculator.R"
 
 
-@format_placeholder(
-    mutate_helpers_clonesize=MUTATE_HELPERS_CLONESIZE_INDENTED,
-    envs_section_each=ENVS_SECTION_EACH_INDENTED,
+@mark(
+    deprecated=(
+        "[{proc.name}] is deprecated, "
+        "use [SeuratClusterStats] or [ClonalStats] instead."
+    )
 )
 class CellsDistribution(Proc):
     """Distribution of cells (i.e. in a TCR clone) from different groups
@@ -846,7 +854,6 @@ class CellsDistribution(Proc):
         mutaters (type=json): The mutaters to mutate the metadata
             Keys are the names of the mutaters and values are the R expressions
             passed by `dplyr::mutate()` to mutate the metadata.
-            %(mutate_helpers_clonesize)s
 
         cluster_orderby: The order of the clusters to show on the plot.
             An expression passed to `dplyr::summarise()` on the grouped data frame (by `seurat_clusters`).
@@ -889,7 +896,6 @@ class CellsDistribution(Proc):
             value as the case/section name.
         section: The section to show in the report. This allows different cases to be put in the same section in report.
             Only works when `each` is not specified.
-            %(envs_section_each)s
         overlap (list): Plot the overlap of cell groups (values of `cells_by`) in different cases
             under the same section.
             The section must have at least 2 cases, each case should have a single `cells_by` column.
@@ -936,7 +942,6 @@ class CellsDistribution(Proc):
     }
 
 
-@format_placeholder(mutate_helpers_clonesize=MUTATE_HELPERS_CLONESIZE_INDENTED)
 class SeuratMetadataMutater(Proc):
     """Mutate the metadata of the seurat object
 
@@ -947,12 +952,11 @@ class SeuratMetadataMutater(Proc):
             cells.
 
     Output:
-        rdsfile: The seurat object with the additional metadata
+        outfile: The seurat object with the additional metadata
 
     Envs:
         mutaters (type=json): The mutaters to mutate the metadata.
             The key-value pairs will be passed the `dplyr::mutate()` to mutate the metadata.
-            %(mutate_helpers_clonesize)s
 
     Requires:
         r-seurat:
@@ -964,12 +968,13 @@ class SeuratMetadataMutater(Proc):
     """  # noqa: E501
 
     input = "srtobj:file, metafile:file"
-    output = "rdsfile:file:{{in.srtobj | stem}}.RDS"
+    output = "outfile:file:{{in.srtobj | stem}}.qs"
     lang = config.lang.rscript
     envs = {"mutaters": {}}
     script = "file://../scripts/scrna/SeuratMetadataMutater.R"
 
 
+@mark(deprecated="[{proc.name}] is deprecated, use [SeuratClusterStats] instead.")
 class DimPlots(Proc):
     """Seurat - Dimensional reduction plots
 
@@ -999,9 +1004,6 @@ class DimPlots(Proc):
     }
 
 
-@format_placeholder(
-    mutate_helpers_clonesize=MUTATE_HELPERS_CLONESIZE_INDENTED,
-)
 class MarkersFinder(Proc):
     """Find markers between different groups of cells
 
@@ -1026,21 +1028,24 @@ class MarkersFinder(Proc):
             * Used in `future::plan(strategy = "multicore", workers = <ncores>)` to parallelize some Seurat procedures.
             * See also: <https://satijalab.org/seurat/articles/future_vignette.html>
         mutaters (type=json): The mutaters to mutate the metadata
-            %(mutate_helpers_clonesize)s
-        ident-1: The first group of cells to compare
-        ident-2: The second group of cells to compare
-            If not provided, the rest of the cells are used for `ident-2`.
         group-by: The column name in metadata to group the cells.
             If only `group-by` is specified, and `ident-1` and `ident-2` are
             not specified, markers will be found for all groups in this column
             in the manner of "group vs rest" comparison.
             `NA` group will be ignored.
+            If `None`, `Seurat::Idents(srtobj)` will be used, which is usually
+            `"seurat_clusters"` after unsupervised clustering.
+        ident-1: The first group of cells to compare
+            When this is empty, the comparisons will be expanded to each group v.s. the rest of the cells in `group-by`.
+        ident-2: The second group of cells to compare
+            If not provided, the rest of the cells are used for `ident-2`.
         each: The column name in metadata to separate the cells into different
             cases.
-        prefix_each (flag): Whether to prefix the `each` column name to the
-            value as the case/section name.
-        prefix_group (flag): When neither `ident-1` nor `ident-2` is specified,
-            should we prefix the group name to the section name?
+            When this is specified, the case will be expanded for each value of
+            the column in metadata. For example, when you have `envs.cases."Cluster Markers".each = "Sample"`,
+            then the case will be expanded as `envs.cases."Cluster Markers - Sample1"`, `envs.cases."Cluster Markers - Sample2"`, etc.
+            You can specify `allmarker_plots` and `overlaps` to plot the markers for all cases in the same plot and plot the overlaps of the markers
+            between different cases by values in this column.
         dbs (list): The dbs to do enrichment analysis for significant
             markers See below for all libraries.
             <https://maayanlab.cloud/Enrichr/#libraries>
@@ -1050,24 +1055,28 @@ class MarkersFinder(Proc):
             `p_val_adj`. For example, `"p_val_adj < 0.05 & abs(avg_log2FC) > 1"`
             to select markers with adjusted p-value < 0.05 and absolute log2
             fold change > 1.
+        enrich_style (choice): The style of the enrichment analysis.
+            The enrichment analysis will be done by `EnrichIt()` from [`enrichit`](https://pwwang.github.io/enrichit/).
+            Two styles are available:
+            - enrichr: `enrichr` style enrichment analysis (fisher's exact test will be used).
+            - clusterprofiler: `clusterProfiler` style enrichment analysis (hypergeometric test will be used).
+            - clusterProfiler: alias for `clusterprofiler`
         assay: The assay to use.
         error (flag): Error out if no/not enough markers are found or no pathways are enriched.
             If `False`, empty results will be returned.
-        site: The site to use for the `enrichR` enrichment analysis.
         subset: An expression to subset the cells for each case.
-        cache (type=auto): Where to cache to `FindAllMarkers` results.
+        cache (type=auto): Where to cache the results.
             If `True`, cache to `outdir` of the job. If `False`, don't cache.
             Otherwise, specify the directory to cache to.
         rest (ns): Rest arguments for `Seurat::FindMarkers()`.
             Use `-` to replace `.` in the argument name. For example,
             use `min-pct` instead of `min.pct`.
-            This only works when `use_presto` is `False`.
             - <more>: See <https://satijalab.org/seurat/reference/findmarkers>
         allmarker_plots_defaults (ns): Default options for the plots for all markers when `ident-1` is not specified.
             - plot_type: The type of the plot.
                 See <https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html>.
                 Available types are `violin`, `box`, `bar`, `ridge`, `dim`, `heatmap` and `dot`.
-            - more_formats (list): The extra formats to save the plot in.
+            - more_formats (type=list): The extra formats to save the plot in.
             - save_code (flag): Whether to save the code to generate the plot.
             - devpars (ns): The device parameters for the plots.
                 - res (type=int): The resolution of the plots.
@@ -1078,12 +1087,22 @@ class MarkersFinder(Proc):
             - <more>: Other arguments passed to [`scplotter::FeatureStatPlot()`](https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html).
         allmarker_plots (type=json): All marker plot cases.
             The keys are the names of the cases and the values are the dicts inherited from `allmarker_plots_defaults`.
+        allenrich_plots_defaults (ns): Default options for the plots to generate for the enrichment analysis.
+            - plot_type: The type of the plot.
+            - devpars (ns): The device parameters for the plots.
+                - res (type=int): The resolution of the plots.
+                - height (type=int): The height of the plots.
+                - width (type=int): The width of the plots.
+            - <more>: See <https://pwwang.github.io/scplotter/reference/EnrichmentPlot.html>.
+        allenrich_plots (type=json): Cases of the plots to generate for the enrichment analysis.
+            The keys are the names of the cases and the values are the dicts inherited from `allenrich_plots_defaults`.
+            The cases under `envs.cases` can inherit this options.
         marker_plots_defaults (ns): Default options for the plots to generate for the markers.
             - plot_type: The type of the plot.
                 See <https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html>.
                 Available types are `violin`, `box`, `bar`, `ridge`, `dim`, `heatmap` and `dot`.
                 There are two additional types available - `volcano_pct` and `volcano_log2fc`.
-            - more_formats (list): The extra formats to save the plot in.
+            - more_formats (type=list): The extra formats to save the plot in.
             - save_code (flag): Whether to save the code to generate the plot.
             - devpars (ns): The device parameters for the plots.
                 - res (type=int): The resolution of the plots.
@@ -1096,11 +1115,12 @@ class MarkersFinder(Proc):
                 [`scplotter::VolcanoPlot()`](https://pwwang.github.io/plotthis/reference/VolcanoPlot.html).
         marker_plots (type=json): Cases of the plots to generate for the markers.
             Plot cases. The keys are the names of the cases and the values are the dicts inherited from `marker_plots_defaults`.
+            The cases under `envs.cases` can inherit this options.
         enrich_plots_defaults (ns): Default options for the plots to generate for the enrichment analysis.
             - plot_type: The type of the plot.
                 See <https://pwwang.github.io/scplotter/reference/EnrichmentPlot.html>.
                 Available types are `bar`, `dot`, `lollipop`, `network`, `enrichmap` and `wordcloud`.
-            - more_formats (list): The extra formats to save the plot in.
+            - more_formats (type=list): The extra formats to save the plot in.
             - save_code (flag): Whether to save the code to generate the plot.
             - devpars (ns): The device parameters for the plots.
                 - res (type=int): The resolution of the plots.
@@ -1109,44 +1129,33 @@ class MarkersFinder(Proc):
             - <more>: See <https://pwwang.github.io/scplotter/reference/EnrichmentPlot.htmll>.
         enrich_plots (type=json): Cases of the plots to generate for the enrichment analysis.
             The keys are the names of the cases and the values are the dicts inherited from `enrich_plots_defaults`.
-        cases (type=json): If you have multiple cases for marker discovery, you can specify them
-            here. The keys are the names of the cases and the values are the above options. If some options are
-            not specified, the default values specified above (under `envs`) will be used.
-            If no cases are specified, the default case will be added with the default values under `envs` with the name `DEFAULT`.
-            If you want to put some cases under the same section in the report, you can specify the section name in the case name
-            as a prefix separated by `::`. For example, `section1::case1` and `section1::case2` will be put `case1` and `case2`
-            under the section `section1`.
-        overlaps_defaults (ns): Default options for investigating the overlapping of significant markers between different cases.
-            - cases (list): The cases to do the overlapping analysis, including the prefix section name.
-                The case must have `ident-1` specified. When `each` is specified, the case will be expanded.
-                For example, `case1` with `each = "group"`, where `group` has `g1` and `g2`, will be expanded to
-                `case1::g1` and `case1::g2`, or `case1::group - g1` and `case1::group - g2` if `prefix_each` is `True`.
-                There must be at least 2 cases to do the overlapping analysis.
+            The cases under `envs.cases` can inherit this options.
+        overlaps_defaults (ns): Default options for investigating the overlapping of significant markers between different cases or comparisons.
+            This means either `ident-1` should be empty, so that they can be expanded to multiple comparisons.
             - sigmarkers: The expression to filter the significant markers for each case.
                 If not provided, `envs.sigmarkers` will be used.
-            - venn (ns): The options for the Venn diagram.
-                - enabled (flag): Whether to enable the Venn diagram.
-                    Default is "auto", which means enabled when there are no more than 5 cases.
-                - more_formats (list): The extra formats to save the plot in.
-                - save_code (flag): Whether to save the code to generate the plot.
-                - devpars (ns): The device parameters for the plots.
-                    - res (type=int): The resolution of the plots.
-                    - height (type=int): The height of the plots.
-                    - width (type=int): The width of the plots.
-                - <more>: More arguments pased to `plotthis::VennDiagram()`.
-                    https://pwwang.github.io/plotthis/reference/venndiagram1.html
-            - upset (ns): The options for the UpSet plot.
-                - enabled (flag): Whether to enable the UpSet plot.
-                - more_formats (list): The extra formats to save the plot in.
-                - save_code (flag): Whether to save the code to generate the plot.
-                - devpars (ns): The device parameters for the plots.
-                    - res (type=int): The resolution of the plots.
-                    - height (type=int): The height of the plots.
-                    - width (type=int): The width of the plots.
-                - <more>: More arguments pased to `plotthis::UpsetPlot()`.
-                    https://pwwang.github.io/plotthis/reference/upsetplot1.html
-        overlaps (type=json): Cases for investigating the overlapping of significant markers between different cases.
+            - plot_type (choice): The type of the plot to generate for the overlaps.
+                - venn: Use `plotthis::VennDiagram()`.
+                - upset: Use `plotthis::UpsetPlot()`.
+            - more_formats (type=list): The extra formats to save the plot in.
+            - save_code (flag): Whether to save the code to generate the plot.
+            - devpars (ns): The device parameters for the plots.
+                - res (type=int): The resolution of the plots.
+                - height (type=int): The height of the plots.
+                - width (type=int): The width of the plots.
+            - <more>: More arguments pased to `plotthis::VennDiagram()`
+                (<https://pwwang.github.io/plotthis/reference/venndiagram1.html>)
+                or `plotthis::UpsetPlot()`
+                (<https://pwwang.github.io/plotthis/reference/upsetplot1.html>)
+        overlaps (type=json): Cases for investigating the overlapping of significant markers between different cases or comparisons.
             The keys are the names of the cases and the values are the dicts inherited from `overlaps_defaults`.
+            There are two situations that we can perform overlaps:
+            1. If `ident-1` is not specified, the overlaps can be performed between different comparisons.
+            2. If `each` is specified, the overlaps can be performed between different cases, where in each case, `ident-1` must be specified.
+        cases (type=json): If you have multiple cases for marker discovery, you can specify them
+            here. The keys are the names of the cases and the values are the above options. If some options are
+            not specified, the default values specified above (under `envs`) will be used.
+            If no cases are specified, the default case will be added with the default values under `envs` with the name `Marker Discovery`.
     """  # noqa: E501
 
     input = "srtobj:file"
@@ -1155,20 +1164,18 @@ class MarkersFinder(Proc):
     envs = {
         "ncores": config.misc.ncores,
         "mutaters": {},
+        "group-by": None,
         "ident-1": None,
         "ident-2": None,
-        "group-by": "seurat_clusters",
         "each": None,
-        "prefix_each": True,
-        "prefix_group": True,
-        "assay": None,
-        "subset": None,
-        "error": True,
-        "site": "Enrichr",
-        "rest": {},
         "dbs": ["KEGG_2021_Human", "MSigDB_Hallmark_2020"],
         "sigmarkers": "p_val_adj < 0.05",
+        "enrich_style": "enrichr",
+        "assay": None,
+        "error": True,
+        "subset": None,
         "cache": config.path.tmpdir,
+        "rest": {},
         "allmarker_plots_defaults": {
             "plot_type": None,
             "more_formats": [],
@@ -1178,6 +1185,11 @@ class MarkersFinder(Proc):
             "genes": 10,
         },
         "allmarker_plots": {},
+        "allenrich_plots_defaults": {
+            "plot_type": "heatmap",
+            "devpars": {"res": 100},
+        },
+        "allenrich_plots": {},
         "marker_plots_defaults": {
             "plot_type": None,
             "more_formats": [],
@@ -1199,24 +1211,15 @@ class MarkersFinder(Proc):
         "enrich_plots": {
             "Bar Plot": {"plot_type": "bar", "ncol": 1, "top_term": 10},
         },
-        "cases": {},
         "overlaps_defaults": {
-            "cases": [],
             "sigmarkers": None,
-            "venn": {
-                "enabled": "auto",
-                "more_formats": [],
-                "save_code": False,
-                "devpars": {"res": 100},
-            },
-            "upset": {
-                "enabled": True,
-                "more_formats": [],
-                "save_code": False,
-                "devpars": {"res": 100},
-            },
+            "plot_type": "venn",
+            "more_formats": [],
+            "save_code": False,
+            "devpars": {"res": 100},
         },
         "overlaps": {},
+        "cases": {},
     }
     order = 5
     script = "file://../scripts/scrna/MarkersFinder.R"
@@ -1230,7 +1233,7 @@ class TopExpressingGenes(Proc):
     """Find the top expressing genes in each cluster
 
     Input:
-        srtobj: The seurat object in RDS format
+        srtobj: The seurat object in RDS or qs/qs2 format
 
     Output:
         outdir: The output directory for the tables and plots
@@ -1245,27 +1248,38 @@ class TopExpressingGenes(Proc):
         group-by: The column name in metadata to group the cells.
         each: The column name in metadata to separate the cells into different
             cases.
-            When specified, `ident` must be specified
-        prefix_each (flag): Whether to prefix the `each` column name to the
-            value as the case/section name.
-        section: The section name for the report.
-            Worked only when `each` is not specified and `ident` is specified.
-            Otherwise, the section name will be constructed from `each` and
-            `group-by`.
-            If `DEFAULT`, and it's the only section, it not included in the
-            case/section names.
         dbs (list): The dbs to do enrichment analysis for significant
             markers See below for all libraries.
             <https://maayanlab.cloud/Enrichr/#libraries>
         n (type=int): The number of top expressing genes to find.
+        enrich_style (choice): The style of the enrichment analysis.
+            The enrichment analysis will be done by `EnrichIt()` from [`enrichit`](https://pwwang.github.io/enrichit/).
+            Two styles are available:
+            - enrichr: `enrichr` style enrichment analysis (fisher's exact test will be used).
+            - clusterprofiler: `clusterProfiler` style enrichment analysis (hypergeometric test will be used).
+            - clusterProfiler: alias for `clusterprofiler`
+        enrich_plots_defaults (ns): Default options for the plots to generate for the enrichment analysis.
+            - plot_type: The type of the plot.
+                See <https://pwwang.github.io/scplotter/reference/EnrichmentPlot.html>.
+                Available types are `bar`, `dot`, `lollipop`, `network`, `enrichmap` and `wordcloud`.
+            - more_formats (type=list): The extra formats to save the plot in.
+            - save_code (flag): Whether to save the code to generate the plot.
+            - devpars (ns): The device parameters for the plots.
+                - res (type=int): The resolution of the plots.
+                - height (type=int): The height of the plots.
+                - width (type=int): The width of the plots.
+            - <more>: See <https://pwwang.github.io/scplotter/reference/EnrichmentPlot.htmll>.
+        enrich_plots (type=json): Cases of the plots to generate for the enrichment analysis.
+            The keys are the names of the cases and the values are the dicts inherited from `enrich_plots_defaults`.
+            The cases under `envs.cases` can inherit this options.
         subset: An expression to subset the cells for each case.
         cases (type=json): If you have multiple cases, you can specify them
             here. The keys are the names of the cases and the values are the
             above options except `mutaters`. If some options are
             not specified, the default values specified above will be used.
             If no cases are specified, the default case will be added with
-            the default values under `envs` with the name `DEFAULT`.
-    """
+            the default values under `envs` with the name `Top Expressing Genes`.
+    """  # noqa: E501
 
     input = "srtobj:file"
     output = "outdir:dir:{{in.srtobj | stem}}.top_expressing_genes"
@@ -1274,13 +1288,20 @@ class TopExpressingGenes(Proc):
     envs = {
         "mutaters": {},
         "ident": None,
-        "group-by": "seurat_clusters",
+        "group-by": None,
         "each": None,
-        "prefix_each": True,
-        "section": "DEFAULT",
         "dbs": ["KEGG_2021_Human", "MSigDB_Hallmark_2020"],
         "n": 250,
         "subset": None,
+        "enrich_style": "enrichr",
+        "enrich_plots_defaults": {
+            "more_formats": [],
+            "save_code": False,
+            "devpars": {"res": 100},
+        },
+        "enrich_plots": {
+            "Bar Plot": {"plot_type": "bar", "ncol": 1, "top_term": 10},
+        },
         "cases": {},
     }
     plugin_opts = {
@@ -1301,7 +1322,7 @@ class ExprImputation(Proc):
     - [Dijk, David van, et al. "MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data." BioRxiv (2017): 111591.](https://www.cell.com/cell/abstract/S0092-8674(18)30724-4)
 
     Input:
-        infile: The input file in RDS format of Seurat object
+        infile: The input file in RDS/qs format of Seurat object
 
     Output:
         outfile: The output file in RDS format of Seurat object
@@ -1321,6 +1342,9 @@ class ExprImputation(Proc):
             - refgene: The reference gene file
         rmagic_args (ns): The arguments for rmagic
             - python: The python path where magic-impute is installed.
+            - threshold (type=float): The threshold for magic imputation.
+              Only the genes with dropout rates greater than this threshold (No. of
+              cells with non-zero expression / total number of cells) will be imputed.
         alra_args (type=json): The arguments for `RunALRA()`
 
     Requires:
@@ -1353,11 +1377,11 @@ class ExprImputation(Proc):
     """  # noqa: E501
 
     input = "infile:file"
-    output = "outfile:file:{{in.infile | stem}}.imputed.RDS"
+    output = "outfile:file:{{in.infile | stem}}.imputed.qs"
     lang = config.lang.rscript
     envs = {
         "tool": "alra",
-        "rmagic_args": {"python": config.exe.magic_python},
+        "rmagic_args": {"python": config.exe.magic_python, "threshold": 0.5},
         "scimpute_args": {
             "drop_thre": 0.5,
             "kcluster": None,
@@ -1556,10 +1580,6 @@ class SeuratTo10X(Proc):
     script = "file://../scripts/scrna/SeuratTo10X.R"
 
 
-@format_placeholder(
-    mutate_helpers_clonesize=MUTATE_HELPERS_CLONESIZE_INDENTED,
-    envs_section_each=ENVS_SECTION_EACH_INDENTED,
-)
 class ScFGSEA(Proc):
     """Gene set enrichment analysis for cells in different groups using `fgsea`
 
@@ -1588,17 +1608,12 @@ class ScFGSEA(Proc):
             Passed to `nproc` of `fgseaMultilevel()`.
         mutaters (type=json): The mutaters to mutate the metadata.
             The key-value pairs will be passed the `dplyr::mutate()` to mutate the metadata.
-            %(mutate_helpers_clonesize)s
 
         group-by: The column name in metadata to group the cells.
         ident-1: The first group of cells to compare
         ident-2: The second group of cells to compare, if not provided, the rest of the cells that are not `NA`s in `group-by` column are used for `ident-2`.
         each: The column name in metadata to separate the cells into different subsets to do the analysis.
-        prefix_each (flag): Whether to prefix the `each` column name to the values as the case/section name.
         subset: An expression to subset the cells.
-        section: The section name for the report. Worked only when `each` is not specified. Otherwise, the section name will be constructed from `each` and its value.
-            This allows different cases to be put into the same section in the report.
-            %(envs_section_each)s
         gmtfile: The pathways in GMT format, with the gene names/ids in the same format as the seurat object.
             One could also use a URL to a GMT file. For example, from <https://download.baderlab.org/EM_Genesets/current_release/Human/symbol/Pathways/>.
         method (choice): The method to do the preranking.
@@ -1622,6 +1637,15 @@ class ScFGSEA(Proc):
             If it is < 1, will apply it to `padj`, selecting pathways with `padj` < `top`.
         eps (type=float): This parameter sets the boundary for calculating the p value.
             See <https://rdrr.io/bioc/fgsea/man/fgseaMultilevel.html>
+        allpathway_plots_defaults (ns): Default options for the plots to generate for all pathways.
+            - plot_type: The type of the plot, currently either dot or heatmap (default)
+            - devpars (ns): The device parameters for the plots.
+                - res (type=int): The resolution of the plots.
+                - height (type=int): The height of the plots.
+                - width (type=int): The width of the plots.
+            - <more>: See <https://pwwang.github.io/biopipen.utils.R/reference/VizGSEA.html>.
+        allpathway_plots (type=json): Cases of the plots to generate for all pathways.
+            The keys are the names of the cases and the values are the dicts inherited from `allpathway_plots_defaults`.
         minsize (type=int): Minimal size of a gene set to test. All pathways below the threshold are excluded.
         maxsize (type=int): Maximal size of a gene set to test. All pathways above the threshold are excluded.
         rest (type=json;order=98): Rest arguments for [`fgsea()`](https://rdrr.io/bioc/fgsea/man/fgsea.html)
@@ -1629,7 +1653,7 @@ class ScFGSEA(Proc):
         cases (type=json;order=99): If you have multiple cases, you can specify them here.
             The keys are the names of the cases and the values are the above options except `mutaters`.
             If some options are not specified, the default values specified above will be used.
-            If no cases are specified, the default case will be added with the name `DEFAULT`.
+            If no cases are specified, the default case will be added with the name `GSEA`.
 
     Requires:
         bioconductor-fgsea:
@@ -1648,21 +1672,24 @@ class ScFGSEA(Proc):
         "ident-1": None,
         "ident-2": None,
         "each": None,
-        "prefix_each": True,
         "subset": None,
-        "section": "DEFAULT",
-        "gmtfile": "",
+        "gmtfile": "KEGG_2021_Human",
         "method": "s2n",
         "top": 20,
         "minsize": 10,
         "maxsize": 100,
         "eps": 0,
+        "allpathway_plots_defaults": {
+            "plot_type": "heatmap",
+            "devpars": {"res": 100},
+        },
+        "allpathway_plots": {},
         "rest": {},
         "cases": {},
     }
     script = "file://../scripts/scrna/ScFGSEA.R"
     plugin_opts = {
-        "report": "file://../reports/scrna/ScFGSEA.svelte",
+        "report": "file://../reports/common.svelte",
         "report_paging": 8,
     }
 
@@ -1701,10 +1728,10 @@ class CellTypeAnnotation(Proc):
         ```
 
     Input:
-        sobjfile: The seurat object
+        sobjfile: The single-cell object in RDS/qs/qs2/h5ad format.
 
     Output:
-        outfile: The rds file of seurat object with cell type annotated.
+        outfile: The rds/qs/qs2/h5ad file of seurat object with cell type annotated.
             A text file containing the mapping from the old `seurat_clusters` to the new cell types
             will be generated and saved to `cluster2celltype.tsv` under the job output directory.
 
@@ -1761,6 +1788,8 @@ class CellTypeAnnotation(Proc):
                 at the cost of increased runtime.
             - over_clustering (type=auto): The column name in metadata to use as clusters for majority voting.
                 Set to `False` to disable over-clustering.
+                When `in.sobjfile` is rds/qs/qs2 (supposing we have a Seurat object), the default ident is used by default.
+                Otherwise, it is False by default.
             - assay: When converting a Seurat object to AnnData, the assay to use.
                 If input is h5seurat, this defaults to RNA.
                 If input is Seurat object in RDS, this defaults to the default assay.
@@ -1773,7 +1802,8 @@ class CellTypeAnnotation(Proc):
             An RDS file will be generated for other tools.
             - input: Use the same file type as the input.
             - rds: Use RDS file.
-            - h5seurat: Use h5seurat file.
+            - qs: Use qs2 file.
+            - qs2: Use qs2 file.
             - h5ad: Use AnnData file.
 
     Requires:
@@ -1816,7 +1846,7 @@ class CellTypeAnnotation(Proc):
             "model": None,
             "python": config.lang.python,
             "majority_voting": True,
-            "over_clustering": "seurat_clusters",
+            "over_clustering": None,
             "assay": None,
         },
         "merge": False,
@@ -1860,8 +1890,9 @@ class SeuratMap2Ref(Proc):
             The file type is determined by the extension. `.rds` or `.RDS` for
             RDS file, `.h5seurat` or `.h5` for h5seurat file.
         refnorm (choice): Normalization method the reference used. The same method will be used for the query.
-            - NormalizeData: Using [`NormalizeData`](https://satijalab.org/seurat/reference/normalizedata).
+            - LogNormalize: Using [`NormalizeData`](https://satijalab.org/seurat/reference/normalizedata).
             - SCTransform: Using [`SCTransform`](https://satijalab.org/seurat/reference/sctransform).
+            - SCT: Alias of SCTransform.
             - auto: Automatically detect the normalization method.
                 If the default assay of reference is `SCT`, then `SCTransform` will be used.
         split_by: The column name in metadata to split the query into multiple objects.
@@ -1900,9 +1931,19 @@ class SeuratMap2Ref(Proc):
             - refdata (type=json): Extra data to transfer from the reference to the query.
             - <more>: See <https://satijalab.org/seurat/reference/mapquery>.
                 Note that the hyphen (`-`) will be transformed into `.` for the keys.
-        MappingScore (ns): Arguments for [`MappingScore()`](https://satijalab.org/seurat/reference/mappingscore)
-            - <more>: See <https://satijalab.org/seurat/reference/mappingscore>.
-                Note that the hyphen (`-`) will be transformed into `.` for the keys.
+        cache (type=auto): Whether to cache the information at different steps.
+            If `True`, the seurat object will be cached in the job output directory, which will be not cleaned up when job is rerunning.
+            The cached seurat object will be saved as `<signature>.<kind>.RDS` file, where `<signature>` is the signature determined by
+            the input and envs of the process.
+            See <https://github.com/satijalab/seurat/issues/7849>, <https://github.com/satijalab/seurat/issues/5358> and
+            <https://github.com/satijalab/seurat/issues/6748> for more details also about reproducibility issues.
+            To not use the cached seurat object, you can either set `cache` to `False` or delete the cached file at
+            `<signature>.RDS` in the cache directory.
+        plots (type=json): The plots to generate.
+            The keys are the names of the plots and the values are the arguments for the plot.
+            The arguments will be passed to `biopipen.utils::VizSeuratMap2Ref()` to generate the plots.
+            The plots will be saved to the output directory.
+            See <https://pwwang.github.io/biopipen.utils.R/reference/VizSeuratMap2Ref.html>.
 
     Requires:
         r-seurat:
@@ -1910,8 +1951,9 @@ class SeuratMap2Ref(Proc):
     """  # noqa: E501
 
     input = "sobjfile:file"
-    output = "outfile:file:{{in.sobjfile | stem}}.RDS"
+    output = "outfile:file:{{in.sobjfile | stem}}.qs"
     lang = config.lang.rscript
+    envs_depth = 3
     envs = {
         "ncores": config.misc.ncores,
         "use": None,
@@ -1930,21 +1972,29 @@ class SeuratMap2Ref(Proc):
             "normalization-method": "LogNormalize",
         },
         "FindTransferAnchors": {
-            "reference-reduction": "spca",
+            # "reference-reduction": "spca",
         },
         "MapQuery": {
-            "reference-reduction": "spca",
-            "reduction-model": "wnn.umap",
+            # "reference-reduction": "spca",
+            # "reduction-model": "wnn.umap",
             "refdata": {
                 # "celltype-l1": "celltype.l1",
                 # "celltype-l2": "celltype.l2",
                 # "predicted_ADT": "ADT",
             },
         },
-        "MappingScore": {"ndim": 30},
+        "cache": config.path.tmpdir,
+        "plots": {
+            "Mapped Identity": {
+                "features": "{ident}:{use}",
+            },
+            "Mapping Score": {
+                "features": "{ident}.score",
+            },
+        },
     }
     script = "file://../scripts/scrna/SeuratMap2Ref.R"
-    plugin_opts = {"report": "file://../reports/scrna/SeuratMap2Ref.svelte"}
+    plugin_opts = {"report": "file://../reports/common.svelte"}
 
 
 class RadarPlots(Proc):
@@ -2008,7 +2058,7 @@ class RadarPlots(Proc):
         ///
 
     Input:
-        srtobj: The seurat object in RDS format
+        srtobj: The seurat object in RDS or qs/qs2 format
 
     Output:
         outdir: The output directory for the plots
@@ -2124,10 +2174,7 @@ class RadarPlots(Proc):
     }
 
 
-@format_placeholder(
-    mutate_helpers_clonesize=MUTATE_HELPERS_CLONESIZE_INDENTED,
-    envs_section_each=ENVS_SECTION_EACH_INDENTED,
-)
+@mark(deprecated=True)
 class MetaMarkers(Proc):
     """Find markers between three or more groups of cells, using one-way ANOVA
     or Kruskal-Wallis test.
@@ -2153,7 +2200,6 @@ class MetaMarkers(Proc):
         ncores (type=int): Number of cores to use to parallelize for genes
         mutaters (type=json): The mutaters to mutate the metadata
             The key-value pairs will be passed the `dplyr::mutate()` to mutate the metadata.
-            %(mutate_helpers_clonesize)s
 
         group-by: The column name in metadata to group the cells.
             If only `group-by` is specified, and `idents` are
@@ -2187,7 +2233,6 @@ class MetaMarkers(Proc):
             Worked only when `each` is not specified.
             Otherwise, the section name will be constructed from `each` and `group-by`.
             If `DEFAULT`, and it's the only section, it not included in the case/section names.
-            %(envs_section_each)s
         method (choice): The method for the test.
             - anova: One-way ANOVA
             - kruskal: Kruskal-Wallis test
@@ -2228,7 +2273,7 @@ class Seurat2AnnData(Proc):
     """Convert seurat object to AnnData
 
     Input:
-        sobjfile: The seurat object file, in RDS or h5seurat format
+        sobjfile: The seurat object file, in RDS or qs/qs2 format
 
     Output:
         outfile: The AnnData file
@@ -2249,29 +2294,26 @@ class AnnData2Seurat(Proc):
     """Convert AnnData to seurat object
 
     Input:
-        adfile: The AnnData file
+        adfile: The AnnData .h5ad file
 
     Output:
-        outfile: The seurat object file in RDS format
+        outfile: The seurat object file in RDS or qs/qs2 format
 
     Envs:
         assay: The assay to use to convert to seurat object.
-        outtype (choice): The output file type.
-            - rds: RDS file
-            - h5seurat: h5seurat file
-        dotplot_check (type=auto): Whether to do a check with `Seurat::DotPlot`
+        dotplot_check (type=auto): Whether to do a check with a dot plot.
+            (`scplotter::FeatureStatPlot(plot_type = "dot", ..)` will be used)
             to see if the conversion is successful.
             Set to `False` to disable the check.
             If `True`, top 10 variable genes will be used for the check.
             You can give a list of genes or a string of genes with comma (`,`) separated
             to use for the check.
-            Only works for `outtype = 'rds'`.
     """
 
     input = "adfile:file"
-    output = "outfile:file:{{in.adfile | stem}}.RDS"
+    output = "outfile:file:{{in.adfile | stem}}.qs"
     lang = config.lang.rscript
-    envs = {"outtype": "rds", "assay": "RNA", "dotplot_check": True}
+    envs = {"assay": "RNA", "dotplot_check": True}
     script = "file://../scripts/scrna/AnnData2Seurat.R"
 
 
@@ -2287,7 +2329,7 @@ class ScSimulation(Proc):
             So this could also work as a unique identifier for the simulation (ie. Sample ID).
 
     Output:
-        outfile: The output Seurat object/SingleCellExperiment in RDS format
+        outfile: The output Seurat object/SingleCellExperiment in qs/qs2 format
 
     Envs:
         ngenes (type=int): The number of genes to simulate
@@ -2450,58 +2492,56 @@ class CellCellCommunication(Proc):
 class CellCellCommunicationPlots(Proc):
     """Visualization for cell-cell communication inference.
 
-    R package [`CCPlotR`](https://github.com/Sarah145/CCPlotR) is used to visualize
-    the results.
-
     Input:
         cccfile: The output file from `CellCellCommunication`
-            or a tab-separated file with the following columns: `source`, `target`,
-            `ligand`, `receptor`, and `score`.
-            If so, `in.expfile` can be provided where `exp_df` is needed.
-        expfile: The expression file with the expression of ligands and receptors.
-            Columns include: `cell_type`, `gene` and `mean_exp`.
 
     Output:
         outdir: The output directory for the plots.
 
     Envs:
-        score_col: The column name in the input file that contains the score, if
-            the input file is from `CellCellCommunication`.
-            Two alias columns are added in the result file of `CellCellCommunication`,
-            `mag_score` and `spec_score`, which are the magnitude and specificity
-            scores.
         subset: An expression to pass to `dplyr::filter()` to subset the ccc data.
+        magnitude: The column name in the data to use as the magnitude of the
+            communication. By default, the second last column will be used.
+            See `li.mt.show_methods()` for the available methods in LIANA. or
+            <https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html#Tileplot>
+        specificity: The column name in the data to use as the specificity of the communication.
+            By default, the last column will be used. If the method doesn't have a specificity, set it to None.
+        devpars (ns): The parameters for the plot.
+            - res (type=int): The resolution of the plot
+            - height (type=int): The height of the plot
+            - width (type=int): The width of the plot
+        more_formats (type=list): The additional formats to save the plots.
+        descr: The description of the plot.
         cases (type=json): The cases for the plots.
             The keys are the names of the cases and the values are the arguments for
-            the plots. The arguments include:
-            * kind: one of `arrow`, `circos`, `dotplot`, `heatmap`, `network`,
-                and `sigmoid`.
-            * devpars: The parameters for `png()` for the plot, including `res`,
-                `width`, and `height`.
-            * section: The section name for the report to group the plots.
-            * <other>: Other arguments for `cc_<kind>` function in `CCPlotR`.
-                See the documentation for more details.
-                Or you can use `?CCPlotR::cc_<kind>` in R.
-    """
+            the plots. The arguments include the ones inherited from `envs`.
+        <more>: Other arguments passed to
+            [scplotter::CCCPlot](https://pwwang.github.io/scplotter/reference/CCCPlot.html)
+    """  # noqa: E501
 
-    input = "cccfile:file, expfile:file"
-    output = "outdir:dir:{{in.cccfile | stem}}-ccc_plots"
+    input = "cccfile:file"
+    output = "outdir:dir:{{in.cccfile | stem}}_plots"
     lang = config.lang.rscript
     envs = {
-        "score_col": "mag_score",
         "subset": None,
+        "magnitude": None,
+        "specificity": None,
+        "devpars": {"res": 100},
+        "more_formats": [],
+        "descr": "Cell-cell communication plot",
         "cases": {},
     }
     script = "file://../scripts/scrna/CellCellCommunicationPlots.R"
     plugin_opts = {
-        "report": "file://../reports/scrna/CellCellCommunicationPlots.svelte",
+        "report": "file://../reports/common.svelte",
     }
 
 
 class ScVelo(Proc):
     """Velocity analysis for single-cell RNA-seq data
 
-    This process is implemented based on the Python package `scvelo`.
+    This process is implemented based on the Python package `scvelo` (v0.3.3).
+    Note that it doesn't work with `numpy>=2`.
 
     Input:
         sobjfile: The seurat object file in RDS or h5seurat format or AnnData file.
@@ -2509,18 +2549,20 @@ class ScVelo(Proc):
     Output:
         outfile: The output object with the velocity embeddings and information.
             In either RDS, h5seurat or h5ad format, depending on the `envs.outtype`.
-        outdir: The output directory for the plots
+            There will be also plots generated in the output directory
+            (parent directory of `outfile`).
+            Note that these plots will not be used in the report, but can be used as
+            supplementary information for the velocity analysis.
+            To visualize the velocity embeddings, you can use the `SeuratClusterStats`
+            process with `v_reduction` provided to one of the `envs.dimplots`.
 
     Envs:
         ncores (type=int): Number of cores to use.
         group_by: The column name in metadata to group the cells.
             Typically, this column should be the cluster id.
-        reduction: The nonlinear reduction to use for the velocity analysis.
-            Typically, `umap` will be used.
-            If this is not provided, 'pca' will be used if exists, otherwise a
-            PCA will be performed.
-        modes (type=auto): The modes to use for the analysis.
-            A list or a string with comma separated values.
+        mode (type=list): The mode to use for the velocity analysis.
+            It should be a subset of `['deterministic', 'stochastic', 'dynamical']`,
+            meaning that we can perform the velocity analysis in multiple modes.
         fitting_by (choice): The mode to use for fitting the velocities.
             - stochastic: Stochastic mode
             - deterministic: Deterministic mode
@@ -2528,16 +2570,6 @@ class ScVelo(Proc):
             (both unspliced and spliced) required for a gene.
         n_neighbors (type=int): The number of neighbors to use for the velocity graph.
         n_pcs (type=int): The number of PCs to use for the velocity graph.
-        stream_smooth (type=float): Multiplication factor for scale in Gaussian kernel
-            around grid point.
-        stream_density (type=float): Controls the closeness of streamlines.
-            When density = 2.0, the domain is divided into a 60x60 grid, whereas
-            density linearly scales this grid. Each cell in the grid can have,
-            at most, one traversing streamline. For different densities in each
-            direction, use a tuple (density_x, density_y).
-        arrow_size (type=float): Scaling factor for the arrow size.
-        arrow_length (type=float): Length of arrows.
-        arrow_density (type=float): Density of arrows.
         denoise (flag): Whether to denoise the data.
         denoise_topn (type=int): Number of genes with highest likelihood selected to
             infer velocity directions.
@@ -2546,57 +2578,60 @@ class ScVelo(Proc):
             infer velocity directions.
         calculate_velocity_genes (flag): Whether to calculate the velocity genes.
         top_n (type=int): The number of top features to plot.
-        res (type=int): The resolution of the plots.
         rscript: The path to the Rscript executable used to convert RDS file to AnnData.
             if `in.sobjfile` is an RDS file, it will be converted to AnnData file
             (h5ad). You need `Seurat`, `SeuratDisk` and `digest` installed.
         outtype (choice): The output file type.
-            - input: The same as the input file type.
-            - anndata: AnnData object
-            - h5seurat: h5seurat object
-            - h5ad: h5ad object
+            - <input>: The same as the input file type.
+            - h5seurat: h5seurat file
+            - h5ad: h5ad file
+            - qs: qs/qs2 file
+            - qs2: qs2 file
+            - rds: RDS file
     """
 
     input = "sobjfile:file"
-    output = "outfile:file:{{in.sobjfile | stem}}-scvelo.{{envs.outtype}}"
+    output = (
+        "outfile:file:{{in.sobjfile | stem}}-scvelo."
+        "{{ext0(in.sobjfile) if envs.outtype == '<input>' else envs.outtype}}"
+    )
     lang = config.lang.python
     envs = {
         "ncores": config.misc.ncores,
         "group_by": "seurat_clusters",
-        "reduction": "umap",
-        "modes": ["stochastic", "deterministic", "dynamical"],
+        "mode": ["deterministic", "stochastic", "dynamical"],
         "fitting_by": "stochastic",
         "min_shared_counts": 30,
         "n_neighbors": 30,
         "n_pcs": 30,
-        "stream_smooth": 0.5,
-        "stream_density": 2.0,
-        "arrow_size": 5.0,
-        "arrow_length": 5.0,
-        "arrow_density": 0.5,
         "denoise": False,
         "denoise_topn": 3,
         "kinetics": False,
         "kinetics_topn": 100,
         "calculate_velocity_genes": False,
         "top_n": 6,
-        "res": 100,
         "rscript": config.lang.rscript,
-        "outtype": "input",
+        "outtype": "<input>",
     }
     script = "file://../scripts/scrna/ScVelo.py"
 
 
-class SlingShot(Proc):
-    """Trajectory inference using SlingShot
+class Slingshot(Proc):
+    """Trajectory inference using Slingshot
 
     This process is implemented based on the R package `slingshot`.
 
     Input:
-        sobjfile: The seurat object file in RDS.
+        sobjfile: The seurat object file in RDS or qs format.
 
     Output:
         outfile: The output object with the trajectory information.
+            The lineages are stored in the metadata of the seurat object at
+            columns `LineageX`, where X is the lineage number. The `BranchID`
+            column contains the branch id for each cell.
+            One can use
+            `scplotter::CellDimPlot(object, lineages = c("Lineage1", "Lineage2", ...))`
+            to visualize the trajectories.
 
     Envs:
         group_by: The column name in metadata to group the cells.
@@ -2605,8 +2640,8 @@ class SlingShot(Proc):
         dims (type=auto): The dimensions to use for the analysis.
             A list or a string with comma separated values.
             Consecutive numbers can be specified with a colon (`:`) or a dash (`-`).
-        start: The starting group for the SlingShot analysis.
-        end: The ending group for the SlingShot analysis.
+        start: The starting group for the Slingshot analysis.
+        end: The ending group for the Slingshot analysis.
         prefix: The prefix to add to the column names of the resulting pseudotime variable.
         reverse (flag): Logical value indicating whether to reverse the pseudotime variable.
         align_start (flag): Whether to align the starting pseudotime values at the maximum pseudotime.
@@ -2614,7 +2649,7 @@ class SlingShot(Proc):
     """  # noqa: E501
 
     input = "sobjfile:file"
-    output = "outfile:file:{{in.sobjfile | stem}}.RDS"
+    output = "outfile:file:{{in.sobjfile | stem}}.qs"
     lang = config.lang.rscript
     envs = {
         "group_by": "seurat_clusters",
@@ -2627,7 +2662,7 @@ class SlingShot(Proc):
         "align_start": False,
         "seed": 8525,
     }
-    script = "file://../scripts/scrna/SlingShot.R"
+    script = "file://../scripts/scrna/Slingshot.R"
 
 
 class LoomTo10X(Proc):
@@ -2641,6 +2676,7 @@ class LoomTo10X(Proc):
             including the `matrix.mtx.gz`, `barcodes.tsv.gz` and `features.tsv.gz`
             files.
     """
+
     input = "loomfile:file"
     output = "outdir:dir:{{in.loomfile | stem}}.10X"
     lang = config.lang.rscript