biopipen 0.17.7__tar.gz → 0.18.0__tar.gz

{biopipen-0.17.7 → biopipen-0.18.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.17.7
+Version: 0.18.0
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -13,10 +13,10 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Provides-Extra: runinfo
-Requires-Dist: datar[pandas] (>=0.13,<0.14)
-Requires-Dist: pipen (>=0.10,<0.11)
-Requires-Dist: pipen-board[report] (>=0.11,<0.12)
-Requires-Dist: pipen-cli-run (>=0.9,<0.10)
-Requires-Dist: pipen-filters (>=0.8,<0.9)
-Requires-Dist: pipen-runinfo (>=0.2,<0.3) ; extra == "runinfo"
-Requires-Dist: pipen-verbose (>=0.7,<0.8)
+Requires-Dist: datar[pandas] (>=0.15.2,<0.16.0)
+Requires-Dist: pipen (>=0.11,<0.12)
+Requires-Dist: pipen-board[report] (>=0.12,<0.13)
+Requires-Dist: pipen-cli-run (>=0.10,<0.11)
+Requires-Dist: pipen-filters (>=0.9,<0.10)
+Requires-Dist: pipen-runinfo (>=0.3,<0.4) ; extra == "runinfo"
+Requires-Dist: pipen-verbose (>=0.8,<0.9)

biopipen-0.18.0/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.18.0"

{biopipen-0.17.7 → biopipen-0.18.0}/biopipen/core/filters.py

@@ -107,6 +107,8 @@ def r(
     ignoreintkey: bool = True,
     todot: str = None,
     sortkeys: bool = False,
+    skip: int = 0,
+    _i: int = 0,
 ) -> str:
     """Convert a python object into R repr
 
@@ -117,6 +119,7 @@ def r(
         >>> {"a": 1, "b": 2} -> list(a = 1, b = 2)
 
     Args:
+        obj: The object to convert
         ignoreintkey: When keys of a dict are integers, whether we should
             ignore them. For example, when `True`, `{1: 1, 2: 2}` will be
             translated into `"list(1, 2)"`, but `"list(`1` = 1, `2` = 2)"`
@@ -130,6 +133,10 @@ def r(
             But sometimes, you want to keep orginal order, for example,
             arguments passed the `dplyr::mutate` function. Because the later
             arguments can refer to the earlier ones.
+        skip: Levels to skip for `todot`. For example, `skip=1` will skip
+            the first level of the keys. When `todot` is `"-"`, `skip=1` will
+            convert `{"a-b": {"c-d": 1}}` to ``list(`a-b` = list(`c.d` = 1))``
+        _i: Current level of the keys. Used internally
 
     Returns:
         Then converted string representation of the object
@@ -165,31 +172,37 @@ def r(
             wrapper = "c"
         return "{}({})".format(
             wrapper,
-            ",".join([r(i, ignoreintkey, todot, sortkeys) for i in obj]),
+            ", ".join(
+                [r(i, ignoreintkey, todot, sortkeys, skip, _i + 1) for i in obj]
+            ),
         )
     if isinstance(obj, dict):
         # list allow repeated names
-        return "list({})".format(
-            ",".join(
-                [
-                    "`{0}`={1}".format(k, r(v, ignoreintkey, todot, sortkeys))
-                    if isinstance(k, int) and not ignoreintkey
-                    else r(v, ignoreintkey, todot, sortkeys)
-                    if isinstance(k, int) and ignoreintkey
-                    else "`{0}`={1}".format(
-                        (
-                            str(k)
-                            if not todot
-                            else str(k).replace(todot, ".")
-                        ).split("#")[0],
-                        r(v, ignoreintkey, todot, sortkeys),
-                    )
-                    for k, v in (
-                        sorted(obj.items()) if sortkeys else obj.items()
-                    )
-                ]
-            )
-        )
+        items = []
+        keys = obj.keys()
+        if sortkeys:
+            keys = sorted(keys)
+        for k in keys:
+            v = obj[k]
+            if isinstance(k, int) and not ignoreintkey:
+                item = (
+                    f"`{k}`={r(v, ignoreintkey, todot, sortkeys, skip, _i + 1)}"
+                )
+            elif isinstance(k, int) and ignoreintkey:
+                item = r(v, ignoreintkey, todot, sortkeys, skip, _i + 1)
+            else:
+                key = str(k)
+                if todot and _i >= skip:
+                    key = key.replace(todot, ".")
+                item = (
+                    f"`{key}`="
+                    f"{r(v, ignoreintkey, todot, sortkeys, skip, _i + 1)}"
+                )
+            items.append(item)
+
+        return f"list({', '.join(items)})"
+
     if isinstance(obj, Namespace):
-        return r(vars(obj), ignoreintkey, todot, sortkeys)
+        return r(vars(obj), ignoreintkey, todot, sortkeys, skip, _i)
+
     return repr(obj)

{biopipen-0.17.7 → biopipen-0.18.0}/biopipen/ns/delim.py

@@ -82,7 +82,7 @@ class SampleInfo(Proc):
             - on: The column name in the data for the stats.
                 Default is `Sample`.
                 If there are duplicated values in `on`, and you want to do stats
-                on the unique values, you can use `distinct:` prefix.
+                on the unique values, you can use `distinct:`/`unique:` prefix.
                 For example, `distinct:Patient` will keep only the first
                 duplicated value in `Patient` and do stats on the unique values.
             - group: The column name in the data for the group ids.

{biopipen-0.17.7 → biopipen-0.18.0}/biopipen/ns/scrna.py

@@ -253,50 +253,88 @@ class SeuratClusterStats(Proc):
         outdir: The output directory
 
     Envs:
+        stats_defaults (ns): The default parameters for `stats`.
+            The parameters from the cases can overwrite the default parameters.
+            - frac (flag): Whether to output the fraction of cells instead of number.
+            - pie (flag): Also output a pie chart?
+            - table (flag): Whether to output a table (in tab-delimited format) and in the report.
+            - ident: The column name in metadata to use as the identity.
+            - group-by: The column name in metadata to group the cells.
+                Does NOT support for pie charts.
+            - split-by: The column name in metadata to split the cells into
+                different plots.
+            - subset: An expression to subset the cells, will be passed to
+                `dplyr::filter()` on metadata.
+            - 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.
         stats (type=json): The number/fraction of cells to plot.
-            * `nCells_*` - Number of cells for each cluster.
-                You can specify `by` to group the cells by a metadata column,
-                and `devpars` to specify the device parameters for the plot.
-                You can also specify `filter` to filter the cells under certain
-                conditions using metadata columns.
-            * `fracCells_*` - Fraction of cells for each cluster.
-                Similar to `nCells_*`, but the fraction is calculated
-                instead of the absolute number.
-        features (type=json): The plots for features, include gene expressions,
-            and columns from metadata.
-            * `features` - The set of features (separated by comma) for the plots,
-                unless `features` for those plots is specified.
-                One could also specify a file with features (one per line).
-            * `ridgeplots` - The ridge plots for the features.
-                See [`Seurat::RidgePlot`](https://satijalab.org/seurat/reference/ridgeplot).
-            * `vlnplots` - Violin plots for the features.
-                See [`Seurat::VlnPlot`](https://satijalab.org/seurat/reference/vlnplot).
-                You can have `boxplot` key to add `geom_boxplot()` to the violin plots.
-            * `featureplots` - The feature plots for the features.
-                See [`Seurat::FeaturePlot`](https://satijalab.org/seurat/reference/featureplot).
-            * `dotplot` - Dot plots for the features.
-                See [`Seurat::DotPlot`](https://satijalab.org/seurat/reference/dotplot).
-            * `heatmap` - Heatmap for the features.
-                See [`Seurat::DoHeatmap`](https://satijalab.org/seurat/reference/doheatmap).
-                You can specify `average=True` to plot on the average of the expressions.
-            * `table` - The table for the features, only gene expressions are supported.
-                (supported keys: title, log2, subset and features).
-            * All the above can have `devpars` to define the output figures
-                and `plus` to add elements to the `ggplot` object.
-                You can also have `subset` to subset the data.
-                Multiple cases can be distinguished by `ridgeplots` and
-                `ridgeplots_1`.
-                If no `features` specified, will use `envs.features`. If you want to use
-                the default variant features `VariantFeatures(srtobj)`, specify
-                `features = 20` for the first 20. Or you can also specify the features
-                directly to `features`.
+            Keys are the names of the plots and values are the dicts inherited from `env.stats_defaults`.
+            Here are some examples -
+            >>> {
+            >>>     "nCells_All": {},
+            >>>     "nCells_Sample": {"kind": "num", "group-by": "Sample"},
+            >>>     "fracCells_Sample": {"kind": "frac", "group-by": "Sample"},
+            >>> }
+        features_defaults (ns): The default parameters for `features`.
+            - features: 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)`.
+            - ident: The column name in metadata to use as the identity.
+            - subset: An expression to subset the cells, will be passed to `tidyrseurat::filter()`.
+            - devpars (ns): The device parameters for the plots. Does not work for `table`.
+                - res (type=int): The resolution of the plots.
+                - height (type=int): The height of the plots.
+                - width (type=int): The width of the plots.
+            - plus: The extra elements to add to the `ggplot` object. Does not work for `table`.
+            - group-by: Group cells in different ways (for example, orig.ident). Works for `ridge`, `vln`, and `dot`.
+                It also works for `feature` as `shape.by` being passed to [`Seurat::FeaturePlot`](https://satijalab.org/seurat/reference/featureplot).
+            - split-by: The column name in metadata to split the cells into different plots.
+                It works for `vln`, `feature`, and `dot`.
+            - assay: The assay to use.
+            - slot: The slot to use.
+            - section: The section to put the plot in the report.
+                If not specified, the case title will be used.
+            - ncol: The number of columns for the plots.
+            - kind (choice): The kind of the plot or table.
+                - ridge: Use `Seurat::RidgePlot`.
+                - ridgeplot: Same as `ridge`.
+                - vln: Use `Seurat::VlnPlot`.
+                - vlnplot: Same as `vln`.
+                - violin: Same as `vln`.
+                - violinplot: Same as `vln`.
+                - feature: Use `Seurat::FeaturePlot`.
+                - featureplot: Same as `feature`.
+                - dot: Use `Seurat::DotPlot`.
+                - dotplot: Same as `dot`.
+                - heatmap: Use `Seurat::DoHeatmap`.
+                    You can specify `average=True` to plot on the average of the expressions.
+                - table: The table for the features, only gene expressions are supported.
+                    (supported keys: ident, subset, and features).
+        features (type=json): The plots for features, include gene expressions, and columns from metadata.
+            Keys are the titles of the cases and values are the dicts inherited from `env.features_defaults`. It can also have other parameters from
+            each Seurat function used by `kind`. Note that for argument name with `.`, you should use `-` instead.
+        dimplots_defaults (ns): The default parameters for `dimplots`.
+            - ident: The column name in metadata to use as the identity.
+            - group-by: Same as `ident`. How the points are colored.
+            - split-by: The column name in metadata to split the cells into different plots.
+            - shape-by: The column name in metadata to use as the shape.
+            - 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.
+            - reduction (choice): Which dimensionality reduction to use.
+                - dim: Use `Seurat::DimPlot`.
+                    First searches for `umap`, then `tsne`, then `pca`.
+                - auto: Same as `dim`
+                - umap: Use `Seurat::UMAPPlot`.
+                - tsne: Use `Seurat::TSNEPlot`.
+                - pca: Use `Seurat::PCAPlot`.
+            - <more>: See <https://satijalab.org/seurat/reference/dimplot>
         dimplots (type=json): The dimensional reduction plots.
-            * `<case>` - The case to plot.
-                Keys are the arguments for `Seurat::Dimplot()`, plus `devpars`
-                for the plots. `devpars` is a dictionary with keys `res`,
-                `height` and `width` to specify the resolution, height and
-                width of the plot. The hyphen (`-`) in the keys will be replaced
-                by `.`.
+            Keys are the titles of the plots and values are the dicts inherited from `env.dimplots_defaults`. It can also have other parameters from
+            [`Seurat::DimPlot`](https://satijalab.org/seurat/reference/dimplot).
 
     Requires:
         r-seurat:
@@ -306,17 +344,55 @@ class SeuratClusterStats(Proc):
     output = "outdir:dir:{{in.srtobj | stem}}.cluster_stats"
     lang = config.lang.rscript
     envs = {
+        "stats_defaults": {
+            "frac": False,
+            "pie": False,
+            "table": False,
+            "ident": "seurat_clusters",
+            "group-by": None,
+            "split-by": None,
+            "subset": None,
+            "devpars": {"res": 100, "height": 800, "width": 1000},
+        },
         "stats": {
-            "nCells_All": {},
-            "nCells_Sample": {"by": "Sample"},
-            "fracCells_Sample": {"by": "Sample"},
+            "Number of cells in each cluster": {
+                "pie": True,
+            },
+            "Number of cells in each cluster by Sample": {
+                "group-by": "Sample",
+                "table": True,
+                "frac": True,
+            },
+        },
+        "features_defaults": {
+            "features": None,
+            "ident": "seurat_clusters",
+            "subset": None,
+            "devpars": {"res": 100},
+            "plus": None,
+            "group-by": None,
+            "split-by": None,
+            "assay": None,
+            "section": None,
+            "slot": None,
+            "kind": None,
+            "ncol": 2,
         },
         "features": {},
+        "dimplots_defaults": {
+            "ident": "seurat_clusters",
+            "group-by": None,
+            "split-by": None,
+            "shape-by": None,
+            "reduction": "dim",
+            "devpars": {"res": 100, "height": 800, "width": 1000},
+        },
         "dimplots": {
-            "Ident": {
-                "group-by": "ident",
-                "devpars": {"res": 100, "height": 1000, "width": 1000},
-            }
+            "Dimensional reduction plot": {
+                "label": True,
+                "label-box": True,
+                "repel": True,
+            },
         },
     }
     script = "file://../scripts/scrna/SeuratClusterStats.R"
@@ -691,6 +767,12 @@ 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.
+        volcano_genes (type=auto): The genes to label in the volcano plot if they are
+            significant markers.
+            If `True`, all significant markers will be labeled. If `False`, no
+            genes will be labeled. Otherwise, specify the genes to label.
+            It could be either a string with comma separated genes, or a list
+            of genes.
         section: The section name for the report.
             Worked only when `each` is not specified and `ident-2` is specified.
             Otherwise, the section name will be constructed from `each` and
@@ -728,6 +810,7 @@ class MarkersFinder(Proc):
             "KEGG_2021_Human",
         ],
         "sigmarkers": "p_val_adj < 0.05",
+        "volcano_genes": True,
         "cases": {},
     }
     order = 5

{biopipen-0.17.7 → biopipen-0.18.0}/biopipen/ns/tcr.py

@@ -1126,10 +1126,13 @@ class TESSA(Proc):
         within_sample (flag): Whether the TCR networks are constructed only
             within TCRs from the same sample/patient (True) or with all the
             TCRs in the meta data matrix (False).
+        assay: Which assay to use to extract the expression matrix.
+            Only works if `in.srtobj` is an RDS file of a Seurat object and
+            `envs.reduction` is not provided.
         predefined_b (flag): Whether use the predefined `b` or not.
             Please check the paper of tessa for more details about the b vector.
             If True, the tessa will not update b in the MCMC iterations.
-        max_iter (int): The maximum number of iterations for MCMC.
+        max_iter (type=int): The maximum number of iterations for MCMC.
     """
     input = "immdata:file,srtobj:file"
     output = """outfile:file:
@@ -1143,6 +1146,7 @@ class TESSA(Proc):
     envs = {
         "python": config.lang.python,
         "prefix": "{Sample}_",
+        "assay": "RNA",
         "within_sample": False,
         "predefined_b": False,
         "max_iter": 1000,

{biopipen-0.17.7 → biopipen-0.18.0}/biopipen/reports/scrna/MarkersFinder.svelte

@@ -25,10 +25,21 @@
                     />
             {%- else -%}
                 <h{{h+1}}>Markers</h{{h+1}}>
-                <DataTable
-                    src={{ casedir | joinpaths: "markers.txt" | quote }}
-                    data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                    />
+                <Tabs>
+                    <Tab label="Markers" />
+                    <Tab label="Volcano Plot" />
+                    <svelte:fragment slot="content">
+                        <TabContent>
+                            <DataTable
+                                src={{ casedir | joinpaths: "markers.txt" | quote }}
+                                data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
+                                />
+                        </TabContent>
+                        <TabContent>
+                            <Image src={{ casedir | joinpaths: "volcano.png" | quote }} />
+                        </TabContent>
+                    </svelte:fragment>
+                </Tabs>
 
                 <h{{h+1}}>Enrichment analysis</h{{h+1}}>
                 {{ enrichr_report(casedir) }}
@@ -49,10 +60,21 @@
                         />
                 {%- else -%}
                     <h{{h+2}}>Markers</h{{h+2}}>
-                    <DataTable
-                        src={{ casedir | joinpaths: "markers.txt" | quote }}
-                        data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                        />
+                    <Tabs>
+                        <Tab label="Markers" />
+                        <Tab label="Volcano Plot" />
+                        <svelte:fragment slot="content">
+                            <TabContent>
+                                <DataTable
+                                    src={{ casedir | joinpaths: "markers.txt" | quote }}
+                                    data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
+                                    />
+                            </TabContent>
+                            <TabContent>
+                                <Image src={{ casedir | joinpaths: "volcano.png" | quote }} />
+                            </TabContent>
+                        </svelte:fragment>
+                    </Tabs>
 
                     <h{{h+2}}>Enrichment analysis</h{{h+2}}>
                     {{ enrichr_report(casedir) }}

biopipen-0.18.0/biopipen/reports/scrna/SeuratClusterStats.svelte

@@ -0,0 +1,82 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+{% from_ os import path %}
+<script>
+    import { DataTable, Image } from "$libs";
+    import { Tabs, Tab, TabContent } from "$ccs";
+</script>
+
+{%- macro report_job(job, h=1) -%}
+    {%- set stats_reports_file = job.out.outdir | joinpaths: "stats", "report_toc.json" -%}
+    {%- set features_reports_file = job.out.outdir | joinpaths: "features", "report_toc.json" -%}
+    {%- set dimplots_reports_file = job.out.outdir | joinpaths: "dimplots", "report_toc.json" -%}
+
+    {%- if stats_reports_file | exists -%}
+        {%- set stats = stats_reports_file | config: "json" -%}
+        {% for key, value in stats.items() -%}
+            <h{{h}}>{{key | escape}}</h{{h}}>
+            <Tabs>
+                {% if 'bar' in value -%}
+                    <Tab label="Bar plot" />
+                {% endif -%}
+                {% if 'pie' in value -%}
+                    <Tab label="Pie chart" />
+                {% endif -%}
+                {% if 'table' in value -%}
+                    <Tab label="Table" />
+                {% endif -%}
+                <svelte:fragment slot="content">
+                    {% if 'bar' in value -%}
+                        <TabContent>
+                            <Image src="{{job.out.outdir}}/stats/{{value.bar}}" />
+                        </TabContent>
+                    {% endif -%}
+                    {% if 'pie' in value -%}
+                        <TabContent>
+                            <Image src="{{job.out.outdir}}/stats/{{value.pie}}" />
+                        </TabContent>
+                    {% endif -%}
+                    {% if 'table' in value -%}
+                        <TabContent>
+                            <DataTable src="{{job.out.outdir}}/stats/{{value.table}}"
+                                data={ {{job.out.outdir | joinpaths: "stats", value.table | datatable: sep="\t", nrows=100 }} }
+                                />
+                        </TabContent>
+                    {% endif -%}
+                </svelte:fragment>
+            </Tabs>
+        {%- endfor -%}
+    {%- endif -%}
+
+    {%- if features_reports_file | exists -%}
+        {%- set features = features_reports_file | config: "json" %}
+        {% for key, value in features.items() -%}
+            <h{{h}}>{{key | escape}}</h{{h}}>
+            {% for val in value -%}
+                {% if "name" in val -%}
+                    <h{{h+1}}>{{val.name | escape}}</h{{h+1}}>
+                {%- endif -%}
+                {% if val.kind == "table" -%}
+                    <DataTable src="{{job.out.outdir}}/features/{{val.file}}"
+                        data={ {{job.out.outdir | joinpaths: "features", val.file | datatable: sep="\t", nrows=100 }} }
+                        />
+                {% else -%}
+                    <Image src="{{job.out.outdir}}/features/{{val.file}}" />
+                {% endif -%}
+            {%- endfor -%}
+        {%- endfor -%}
+    {%- endif -%}
+
+    {%- if dimplots_reports_file | exists -%}
+        {%- set dimplots = dimplots_reports_file | config: "json" %}
+        {% for key, value in dimplots.items() -%}
+            <h{{h}}>{{key | escape}}</h{{h}}>
+            <Image src="{{job.out.outdir}}/dimplots/{{value}}" />
+        {%- endfor -%}
+    {%- endif -%}
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+<h1>{{job.in.srtobj | stem}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

{biopipen-0.17.7 → biopipen-0.18.0}/biopipen/scripts/delim/SampleInfo.R

@@ -5,6 +5,7 @@ library(dplyr)
 library(ggplot2)
 library(ggprism)
 library(ggsci)
+library(ggrepel)
 
 infile <- {{in.infile | r}}
 outfile <- {{out.outfile | r}}
@@ -39,8 +40,9 @@ for (name in names(stats)) {
     plotfile <- file.path(outdir, paste0(name, ".png"))
 
     is_continuous <- FALSE
-    if (startsWith(stat$on, "distinct:")) {
-        stat$on <- substring(stat$on, 10)
+    if (startsWith(stat$on, "distinct:") || startsWith(stat$on, "unique:")) {
+        stat$on <- gsub("distinct:", "", stat$on)
+        stat$on <- gsub("unique:", "", stat$on)
         data <- mutdata %>% distinct(!!sym(stat$on), .keep_all = TRUE)
     } else {
         data <- mutdata
@@ -89,14 +91,14 @@ for (name in names(stats)) {
     if (stat$plot == "boxplot" || stat$plot == "box") {
         p <- ggplot(data, aes(x=!!group, y=!!sym(stat$on), fill=!!group)) +
             geom_boxplot(position = "dodge") +
-            scale_fill_ucscgb() +
+            scale_fill_ucscgb(alpha = .8) +
             xlab("")
     } else if (stat$plot == "violin" ||
                stat$plot == "violinplot" ||
                stat$plot == "vlnplot") {
         p <- ggplot(data, aes(x = !!group, y = !!sym(stat$on), fill=!!group)) +
             geom_violin(position = "dodge") +
-            scale_fill_ucscgb() +
+            scale_fill_ucscgb(alpha = .8) +
             xlab("")
     } else if (
         (grepl("violin", stat$plot) || grepl("vln", stat$plot)) &&
@@ -105,12 +107,12 @@ for (name in names(stats)) {
         p <- ggplot(data, aes(x = !!group, y = !!sym(stat$on), fill = !!group)) +
             geom_violin(position = "dodge") +
             geom_boxplot(width = 0.1, position = position_dodge(0.9), fill="white") +
-            scale_fill_ucscgb() +
+            scale_fill_ucscgb(alpha = .8) +
             xlab("")
     } else if (stat$plot == "histogram" || stat$plot == "hist") {
         p <- ggplot(data, aes(x = !!sym(stat$on), fill = !!group)) +
             geom_histogram(bins = 10, position = "dodge", alpha = 0.8, color = "white") +
-            scale_fill_ucscgb()
+            scale_fill_ucscgb(alpha = .8)
     } else if (stat$plot == "pie" || stat$plot == "piechart") {
         if (is.null(stat$each)) {
             data <- data %>% distinct(!!group, .keep_all = TRUE)
@@ -120,19 +122,20 @@ for (name in names(stats)) {
                 group_by(!!sym(stat$each))
         }
         p <- ggplot(
-            data %>%
-                mutate(
-                    ..prop = !!sym(count_on) / sum(!!sym(count_on)),
-                    ..ypos = (cumsum(..prop) - 0.5 * ..prop) * sum(!!sym(count_on))
-                ),
-            aes(x = "", y = !!sym(count_on), fill = !!group)
+            data %>% arrange(!!group),
+            aes(x = "", y = !!sym(count_on), fill = rev(!!group), label = !!sym(count_on))
         ) +
             geom_bar(stat="identity", width=1, color="white") +
             coord_polar("y", start = 0) +
             theme_void() +
             theme(plot.title = element_text(hjust = 0.5)) +
-            geom_text(aes(y = ..ypos, label = !!sym(count_on))) +
-            scale_fill_ucscgb() +
+            geom_label_repel(
+                position = position_stack(vjust = 0.5),
+                color="#333333",
+                fill="#EEEEEE",
+                size=4
+            ) +
+            scale_fill_ucscgb(alpha = .8, name = group) +
             ggtitle(paste0("# ", stat$on))
     } else if (stat$plot == "bar" || stat$plot == "barplot") {
         if (is.null(stat$each)) {
@@ -144,7 +147,7 @@ for (name in names(stats)) {
             data,
             aes(x = !!group, y = !!sym(count_on), fill = !!group)) +
             geom_bar(stat = "identity") +
-            scale_fill_ucscgb() +
+            scale_fill_ucscgb(alpha = .8) +
             ylab(paste0("# ", stat$on))
     } else {
         stop("Unknown plot type: ", stat$plot)