biopipen 0.34.1__py3-none-any.whl → 0.34.3__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.34.1"
+__version__ = "0.34.3"

biopipen/ns/scrna.py

@@ -197,8 +197,8 @@ class SeuratPreparing(Proc):
 
         SCTransform (ns): Arguments for [`SCTransform()`](https://satijalab.org/seurat/reference/sctransform).
             `object` is specified internally, and `-` in the key will be replaced with `.`.
-            - `return-only-var-genes`: Whether to return only variable genes.
-            - `min_cells`: The minimum number of cells that a gene must be expressed in to be kept.
+            - return-only-var-genes: Whether to return only variable genes.
+            - min_cells: The minimum number of cells that a gene must be expressed in to be kept.
                 A hidden argument of `SCTransform` to filter genes.
                 If you try to keep all genes in the `RNA` assay, you can set `min_cells` to `0` and
                 `return-only-var-genes` to `False`.
@@ -491,7 +491,7 @@ class SeuratClusterStats(Proc):
 
         ```toml
         [SeuratClusterStats.envs.stats]
-        nCells_Sample = { group-by = "Sample" }
+        nCells_Sample = { group_by = "Sample" }
         ```
 
         ![nCells_Sample](https://pwwang.github.io/immunopipe/latest/processes/images/SeuratClusterStats_nCells_Sample.png){: width="80%" }
@@ -515,8 +515,6 @@ class SeuratClusterStats(Proc):
         ```toml
         [SeuratClusterStats.envs.dimplots.Idents]
         label = true
-        label-box = true
-        repel = true
         ```
 
         ![dimplots](https://pwwang.github.io/immunopipe/latest/processes/images/SeuratClusterStats_dimplots.png){: width="80%" }
@@ -533,6 +531,8 @@ 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.
+            You can also use the clone selectors to select the TCR clones/clusters.
+            See <https://pwwang.github.io/scplotter/reference/clone_selectors.html>.
         cache (type=auto): Whether to cache the plots.
             Currently only plots for features are supported, since creating the those
             plots can be time consuming.
@@ -566,6 +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.
+            - descr: The description of the plot, showing in the report.
             - 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.
@@ -657,6 +658,7 @@ class SeuratClusterStats(Proc):
         "clustrees": {},
         "stats_defaults": {
             "subset": None,
+            "descr": None,
             "devpars": {"res": 100},
             "more_formats": [],
             "save_code": False,
@@ -665,10 +667,12 @@ class SeuratClusterStats(Proc):
         "stats": {
             "Number of cells in each cluster (Bar Chart)": {
                 "plot_type": "bar",
+                "x_text_angle": 90,
             },
             "Number of cells in each cluster by Sample (Bar Chart)": {
                 "plot_type": "bar",
                 "group_by": "Sample",
+                "x_text_angle": 90,
             },
         },
         "ngenes_defaults": {
@@ -700,7 +704,6 @@ class SeuratClusterStats(Proc):
         "dimplots": {
             "Dimensional reduction plot": {
                 "label": True,
-                "label_insitu": True,
             },
         },
     }
@@ -1007,11 +1010,11 @@ class DimPlots(Proc):
 class MarkersFinder(Proc):
     """Find markers between different groups of cells
 
-    When only `group-by` is specified as `"seurat_clusters"` in
+    When only `group_by` is specified as `"seurat_clusters"` in
     `envs.cases`, the markers will be found for all the clusters.
 
     You can also find the differentially expressed genes between
-    any two groups of cells by setting `group-by` to a different
+    any two groups of cells by setting `group_by` to a different
     column name in metadata. Follow `envs.cases` for more details.
 
     Input:
@@ -1027,17 +1030,19 @@ class MarkersFinder(Proc):
         ncores (type=int): Number of cores to use for parallel computing for some `Seurat` procedures.
             * 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
-        group-by: The column name in metadata to group the cells.
-            If only `group-by` is specified, and `ident-1` and `ident-2` are
+        mutaters (type=json): The mutaters to mutate the metadata.
+            You can also use the clone selectors to select the TCR clones/clusters.
+            See <https://pwwang.github.io/scplotter/reference/clone_selectors.html>.
+        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
+        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.
@@ -1164,9 +1169,9 @@ class MarkersFinder(Proc):
     envs = {
         "ncores": config.misc.ncores,
         "mutaters": {},
-        "group-by": None,
-        "ident-1": None,
-        "ident-2": None,
+        "group_by": None,
+        "ident_1": None,
+        "ident_2": None,
         "each": None,
         "dbs": ["KEGG_2021_Human", "MSigDB_Hallmark_2020"],
         "sigmarkers": "p_val_adj < 0.05",
@@ -1239,13 +1244,15 @@ class TopExpressingGenes(Proc):
         outdir: The output directory for the tables and plots
 
     Envs:
-        mutaters (type=json): The mutaters to mutate the metadata
+        mutaters (type=json): The mutaters to mutate the metadata.
+            You can also use the clone selectors to select the TCR clones/clusters.
+            See <https://pwwang.github.io/scplotter/reference/clone_selectors.html>.
         ident: The group of cells to find the top expressing genes.
-            The cells will be selected by the `group-by` column with this
+            The cells will be selected by the `group_by` column with this
             `ident` value in metadata.
             If not provided, the top expressing genes will be found for all
-            groups of cells in the `group-by` column.
-        group-by: The column name in metadata to group the cells.
+            groups of cells in the `group_by` column.
+        group_by: The column name in metadata to group the cells.
         each: The column name in metadata to separate the cells into different
             cases.
         dbs (list): The dbs to do enrichment analysis for significant
@@ -1288,7 +1295,7 @@ class TopExpressingGenes(Proc):
     envs = {
         "mutaters": {},
         "ident": None,
-        "group-by": None,
+        "group_by": None,
         "each": None,
         "dbs": ["KEGG_2021_Human", "MSigDB_Hallmark_2020"],
         "n": 250,
@@ -1305,7 +1312,7 @@ class TopExpressingGenes(Proc):
         "cases": {},
     }
     plugin_opts = {
-        "report": "file://../reports/scrna/TopExpressingGenes.svelte",
+        "report": "file://../reports/common.svelte",
         "report_paging": 8,
     }
 
@@ -1608,10 +1615,12 @@ 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.
+            You can also use the clone selectors to select the TCR clones/clusters.
+            See <https://pwwang.github.io/scplotter/reference/clone_selectors.html>.
 
-        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`.
+        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.
         subset: An expression to subset the cells.
         gmtfile: The pathways in GMT format, with the gene names/ids in the same format as the seurat object.
@@ -1637,15 +1646,15 @@ 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.
+        alleach_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`.
+        alleach_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 `alleach_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)
@@ -1668,9 +1677,9 @@ class ScFGSEA(Proc):
     envs = {
         "mutaters": {},
         "ncores": config.misc.ncores,
-        "group-by": None,
-        "ident-1": None,
-        "ident-2": None,
+        "group_by": None,
+        "ident_1": None,
+        "ident_2": None,
         "each": None,
         "subset": None,
         "gmtfile": "KEGG_2021_Human",
@@ -1679,11 +1688,11 @@ class ScFGSEA(Proc):
         "minsize": 10,
         "maxsize": 100,
         "eps": 0,
-        "allpathway_plots_defaults": {
+        "alleach_plots_defaults": {
             "plot_type": "heatmap",
             "devpars": {"res": 100},
         },
-        "allpathway_plots": {},
+        "alleach_plots": {},
         "rest": {},
         "cases": {},
     }
@@ -2681,3 +2690,219 @@ class LoomTo10X(Proc):
     output = "outdir:dir:{{in.loomfile | stem}}.10X"
     lang = config.lang.rscript
     script = "file://../scripts/scrna/LoomTo10X.R"
+
+
+class PseudoBulkDEG(Proc):
+    """Pseduo-bulk differential gene expression analysis
+
+    This process performs differential gene expression analysis, instead of
+    on single-cell level, on the pseudo-bulk data, aggregated from the single-cell data.
+
+    Input:
+        sobjfile: The seurat object file in RDS or qs/qs2 format.
+
+    Output:
+        outdir: The output containing the results of the differential gene expression
+            analysis.
+
+    Envs:
+        mutaters (type=json): Mutaters to mutate the metadata of the
+            seurat object. Keys are the new column names and values are the
+            expressions to mutate the columns. These new columns can be
+            used to define your cases.
+            You can also use the clone selectors to select the TCR clones/clusters.
+            See <https://pwwang.github.io/scplotter/reference/clone_selectors.html>.
+        each: The column name in metadata to separate the cells into different cases.
+            When specified, the case will be expanded to multiple cases for
+            each value in the column.
+        subset: An expression in string to subset the cells.
+        aggregate_by: The column names in metadata to aggregate the cells.
+        layer: The layer to pull and aggregate the data.
+        assay: The assay to pull and aggregate the data.
+        error (flag): Error out if no/not enough markers are found or no pathways are enriched.
+            If `False`, empty results will be returned.
+        group_by: The column name in metadata to group the cells.
+        ident_1: The first identity to compare.
+        ident_2: The second identity to compare.
+            If not specified, the rest of the identities will be compared with `ident_1`.
+        paired_by: The column name in metadata to mark the paired samples.
+            For example, subject. If specified, the paired test will be performed.
+        dbs (list): The databases to use for enrichment analysis.
+            The databases are passed to `biopipen.utils::Enrichr()` to do the
+            enrichment analysis. The default databases are `KEGG_2021_Human` and
+            `MSigDB_Hallmark_2020`.
+            See <https://maayanlab.cloud/Enrichr/#libraries> for the available
+            libraries.
+        sigmarkers: An expression passed to `dplyr::filter()` to filter the
+            significant markers for enrichment analysis.
+            The default is `p_val_adj < 0.05`.
+            If `tool = 'DESeq2'`, the variables that can be used for filtering
+            are: `baseMean`, `log2FC`, `lfcSE`, `stat`, `p_val`, `p_val_adj`.
+            If `tool = 'edgeR'`, the variables that can be used for filtering
+            are: `logCPM`, `log2FC`, `LR`, `p_val`, `p_val_adj`.
+        enrich_style (choice): The style of the enrichment analysis.
+            - enrichr: Use `enrichr`-style for the enrichment analysis.
+            - clusterProfiler: Use `clusterProfiler`-style for the enrichment analysis.
+        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 (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.
+            - order_by: an expression to order the markers, passed by `dplyr::arrange()`.
+            - genes: The number of top genes to show or an expression passed to `dplyr::filter()` to filter the genes.
+            - <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 (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.
+            - order_by: an expression to order the markers, passed by `dplyr::arrange()`.
+            - genes: The number of top genes to show or an expression passed to `dplyr::filter()` to filter the genes.
+            - <more>: Other arguments passed to [`scplotter::FeatureStatPlot()`](https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html).
+                If `plot_type` is `volcano_pct` or `volcano_log2fc`, they will be passed to
+                [`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 (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.
+        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.
+            - 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.
+        tool (choice): The method to use for the differential expression analysis.
+            - DESeq2: Use DESeq2 for the analysis.
+            - edgeR: Use edgeR for the analysis.
+        plots_defaults (ns): The default parameters for the plots.
+            - <more>: Parameters passed to `biopipen.utils::VizBulkDEGs()`.
+                See: <https://pwwang.github.io/biopipen.utils.R/reference/VizBulkDEGs.html>
+        plots (type=json): The parameters for the plots.
+            The keys are the names of the plots and the values are the parameters
+            for the plots. The parameters will override the defaults in `plots_defaults`.
+            If not specified, no plots will be generated.
+        cases (type=json): The cases for the analysis.
+            The keys are the names of the cases and the values are the arguments for
+            the analysis. The arguments include the ones inherited from `envs`.
+            If no cases are specified, a default case will be added with
+            the name `DEG Analysis` and the default values specified above.
+    """  # noqa: E501
+    input = "sobjfile:file"
+    output = "outdir:dir:{{in.sobjfile | stem}}.pseudobulk_deg"
+    lang = config.lang.rscript
+    script = "file://../scripts/scrna/PseudoBulkDEG.R"
+    envs = {
+        "mutaters": {},
+        "each": None,
+        "subset": None,
+        "aggregate_by": None,
+        "layer": "counts",
+        "assay": "RNA",
+        "error": True,
+        "group_by": None,
+        "ident_1": None,
+        "ident_2": None,
+        "paired_by": None,
+        "tool": "DESeq2",
+        "dbs": ["KEGG_2021_Human", "MSigDB_Hallmark_2020"],
+        "sigmarkers": "p_val_adj < 0.05",
+        "enrich_style": "enrichr",
+        "allmarker_plots_defaults": {
+            "plot_type": None,
+            "more_formats": [],
+            "save_code": False,
+            "devpars": {"res": 100},
+            "order_by": "desc(abs(log2FC))",
+            "genes": 10,
+        },
+        "allmarker_plots": {},
+        "allenrich_plots_defaults": {
+            "plot_type": "heatmap",
+            "devpars": {"res": 100},
+        },
+        "allenrich_plots": {},
+        "marker_plots_defaults": {
+            "plot_type": None,
+            "more_formats": [],
+            "save_code": False,
+            "devpars": {"res": 100},
+            "order_by": "desc(abs(log2FC))",
+            "genes": 10,
+        },
+        "marker_plots": {
+            "Volcano Plot": {"plot_type": "volcano"},
+        },
+        "enrich_plots_defaults": {
+            "more_formats": [],
+            "save_code": False,
+            "devpars": {"res": 100},
+        },
+        "enrich_plots": {
+            "Bar Plot": {"plot_type": "bar", "ncol": 1, "top_term": 10},
+        },
+        "overlaps_defaults": {
+            "sigmarkers": None,
+            "plot_type": "venn",
+            "more_formats": [],
+            "save_code": False,
+            "devpars": {"res": 100},
+        },
+        "overlaps": {},
+        "cases": {},
+    }
+    plugin_opts = {
+        "report": "file://../reports/common.svelte",
+        "report_paging": 8,
+    }

biopipen/ns/scrna_metabolic_landscape.py

@@ -165,7 +165,7 @@ class MetabolicFeatures(Proc):
             `1`, `2` and `3` in the `group_by` column, we could have
             `comparisons = ["1", "2"]`, which will compare the group `1` with groups
             `2` and `3`, and the group `2` with groups `1` and `3`. We could also
-            have `comparisons = ["1,2", "1,3"]`, which will compare the group `1` with
+            have `comparisons = ["1:2", "1:3"]`, which will compare the group `1` with
             group `2` and group `1` with group `3`.
         fgsea_args (type=json): Other arguments for the `fgsea::fgsea()` function.
             For example, `{"minSize": 15, "maxSize": 500}`.

biopipen/ns/tcr.py

@@ -1749,6 +1749,11 @@ class ScRepCombiningExpression(Proc):
 
     Output:
         outfile: The `Seurat` object with the TCR/BCR data combined
+            In addition to the meta columns added by
+            `scRepertoire::combineExpression()`, a new column `TCR_Presence` will be
+            added to the metadata. It indicates whether the cell has a TCR/BCR
+            sequence or not. The value is `TRUE` if the cell has a TCR/BCR sequence,
+            and `FALSE` otherwise.
 
     Envs:
         cloneCall: How to call the clone - VDJC gene (gene), CDR3 nucleotide (nt),
@@ -1756,10 +1761,10 @@ class ScRepCombiningExpression(Proc):
             a custom variable in the data.
         chain: indicate if both or a specific chain should be used
             e.g. "both", "TRA", "TRG", "IGH", "IGL".
-        group-by: The column label in the combined clones in which clone frequency will
+        group_by: The column label in the combined clones in which clone frequency will
             be calculated. NULL or "none" will keep the format of input.data.
         proportion (flag): Whether to proportion (TRUE) or total frequency (FALSE) of
-            the clone based on the group.by variable.
+            the clone based on the group_by variable.
         filterNA (flag): Method to subset Seurat/SCE object of barcodes without clone
             information
         cloneSize (type=json): The bins for the grouping based on proportion or
@@ -1767,7 +1772,7 @@ class ScRepCombiningExpression(Proc):
             If proportion is FALSE and the cloneSizes are not set high enough based on
             frequency, the upper limit of cloneSizes will be automatically updated.
         addLabel (flag): This will add a label to the frequency header, allowing the
-            user to try multiple group.by variables or recalculate frequencies after
+            user to try multiple group_by variables or recalculate frequencies after
             subsetting the data.
     """
     input = "screpfile:file,srtobj:file"
@@ -1776,7 +1781,7 @@ class ScRepCombiningExpression(Proc):
     envs = {
         "cloneCall": "aa",
         "chain": "both",
-        "group-by": "Sample",
+        "group_by": "Sample",
         "proportion": True,
         "filterNA": False,
         "cloneSize": {

biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte

@@ -34,15 +34,15 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 
 <UnorderedList>
 <ListItem>
-    <a href="../MetabolicPathwayActivity/index.html">MetabolicPathwayActivity</a>
+    <a href="?proc=MetabolicPathwayActivity" class="listitem">MetabolicPathwayActivity</a>
     <Tile><p>Investigating the metabolic pathways of the cells in different subsets and groups.</p></Tile>
 </ListItem>
 <ListItem>
-    <a href="../MetabolicPathwayHeterogeneity/index.html">MetabolicPathwayHeterogeneity</a>
+    <a href="?proc=MetabolicPathwayHeterogeneity" class="listitem">MetabolicPathwayHeterogeneity</a>
     <Tile><p>Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</p></Tile>
 </ListItem>
 <ListItem>
-    MetabolicFeatures (this page)
+    <span class="listitem">MetabolicFeatures (this page)</span>
     <Tile>
     <p>Gene set enrichment analysis against the metabolic pathways for comparisons by different groups in different subsets.</p>
     <p>The metabolic features are actual gene set enrichment analysis (GSEA) results for the metabolic pathways with given comparisons.</p>
@@ -59,3 +59,12 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
+
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte

@@ -34,7 +34,7 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 
 <UnorderedList>
 <ListItem>
-    MetabolicPathwayActivity (this page)
+    <span class="listitem">MetabolicPathwayActivity (this page)</span>
     <Tile>
         <p>Investigating the metabolic pathways of the cells in different subsets and groups.</p>
         <p>The cells are first subset by subsets and then the metabolic activities are examined for each groups in different subsets.</p>
@@ -69,13 +69,13 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
     </Tile>
 </ListItem>
 <ListItem>
-    <a href="../MetabolicPathwayHeterogeneity/index.html">MetabolicPathwayHeterogeneity</a>
+    <a href="?proc=MetabolicPathwayHeterogeneity" class="listitem">MetabolicPathwayHeterogeneity</a>
     <Tile>
         <p>Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</p>
     </Tile>
 </ListItem>
 <ListItem>
-    <a href="../MetabolicFeatures/index.html">MetabolicFeatures</a>
+    <a href="?proc=MetabolicFeatures" class="listitem">MetabolicFeatures</a>
     <Tile>
         <p>Gene set enrichment analysis against the metabolic pathways for comparisons by different groups in different subsets.</p>
     </Tile>
@@ -91,3 +91,12 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
+
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte

@@ -34,13 +34,13 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 
 <UnorderedList>
 <ListItem>
-    <a href="../MetabolicPathwayActivity/index.html">MetabolicPathwayActivity</a>
+    <a href="?proc=MetabolicPathwayActivity" class="listitem">MetabolicPathwayActivity</a>
     <Tile>
     <p>Investigating the metabolic pathways of the cells in different subsets and groups.</p>
     </Tile>
 </ListItem>
 <ListItem>
-    MetabolicPathwayHeterogeneity (this page)
+    <span class="listitem">MetabolicPathwayHeterogeneity (this page)</span>
     <Tile>
     <p>Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</p>
     <p>
@@ -54,7 +54,7 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
     </Tile>
 </ListItem>
 <ListItem>
-    <a href="../MetabolicFeatures/index.html">MetabolicFeatures</a>
+    <a href="?proc=MetabolicFeatures" class="listitem">MetabolicFeatures</a>
     <Tile>
     <p>Gene set enrichment analysis against the metabolic pathways for comparisons by different groups in different subsets.</p>
     </Tile>
@@ -70,3 +70,12 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
+
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>

biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R

@@ -26,15 +26,8 @@ if (is.null(celltypist_args$model)) {
 }
 dir.create(file.path(outdir, "data", "models"), recursive = TRUE, showWarnings = FALSE)
 modelfile <- file.path(outdir, "data", "models", basename(celltypist_args$model))
-if (!file.exists(modelfile)) {
-    file.symlink(celltypist_args$model, modelfile)
-} else {
-    real_modelfile <- normalizePath(Sys.readlink(modelfile))
-    if (real_modelfile != normalizePath(celltypist_args$model)) {
-        file.remove(modelfile)
-        file.symlink(celltypist_args$model, modelfile)
-    }
-}
+suppressWarnings(file.remove(modelfile))
+file.symlink(normalizePath(celltypist_args$model), modelfile)
 
 sobj <- NULL
 if (!endsWith(sobjfile, ".h5ad")) {
@@ -43,7 +36,7 @@ if (!endsWith(sobjfile, ".h5ad")) {
         # find the default ident name in meta.data
         for (col in colnames(sobj@meta.data)) {
             if (!is.factor(sobj@meta.data[[col]])) { next }
-            if (isTRUE(all.equal(Idents(sobj), sobj@meta.data[[col]]))) {
+            if (isTRUE(all.equal(unname(Idents(sobj)), sobj@meta.data[[col]]))) {
                 celltypist_args$over_clustering <- col
                 break
             }