Use diff reg plots

docs/examples_single_analysis/diff_regulation_ancova.ipynb

@@ -50,6 +50,7 @@
     "import pandas as pd\n",
     "import sklearn.impute\n",
     "import vuecore.plots.basic.scatter\n",
+    "from vuecore.interactive import get_differential_regulation_plot\n",
     "\n",
     "import acore.differential_regulation as ad\n",
     "\n",
@@ -350,6 +351,26 @@
     ")\n",
     "scatter_plot_adv"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0fdb7bd6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "get_differential_regulation_plot(\n",
+    "    data=ancova,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1af558dc",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

docs/examples_single_analysis/diff_regulation_ancova.py

@@ -34,6 +34,7 @@
 import pandas as pd
 import sklearn.impute
 import vuecore.plots.basic.scatter
+from vuecore.interactive import get_differential_regulation_plot
 
 import acore.differential_regulation as ad
 
@@ -193,3 +194,10 @@
     height=600,
 )
 scatter_plot_adv
+
+# %%
+get_differential_regulation_plot(
+    data=ancova,
+)
+
+# %%

docs/examples_single_analysis/diff_regulation_anova_ttest_two_groups.ipynb

@@ -44,7 +44,7 @@
    "source": [
     "import dsp_pandas\n",
     "import pandas as pd\n",
-    "import vuecore.plots.basic.scatter\n",
+    "import vuecore.interactive\n",
     "\n",
     "import acore.differential_regulation as ad\n",
     "\n",
@@ -315,7 +315,9 @@
   {
    "cell_type": "markdown",
    "id": "5fb1bebd",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "source": [
     "## View Volcano plot for the ANOVA results\n",
     "- p-value (unadjusted) using the -log10 transformation on the y-axis, using\n",
@@ -332,33 +334,14 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "37085bf1",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 0
+   },
    "outputs": [],
    "source": [
-    "scatter_plot_adv = vuecore.plots.basic.scatter.create_scatter_plot(\n",
-    "    data=anova.reset_index(),\n",
-    "    x=\"log2FC\",\n",
-    "    y=\"-log10 pvalue\",\n",
-    "    color=\"rejected\",\n",
-    "    title=\"Simple Volcano Plot\",\n",
-    "    subtitle=\"Visualizing ANOVA results\",\n",
-    "    labels={\n",
-    "        \"log2FC\": \"Log2 Fold Change\",\n",
-    "        \"-log10 pvalue\": \"-log10(p-value)\",\n",
-    "        \"rejected\": \"FDR corrected Significant\",\n",
-    "        \"identifier\": \"Protein Identifier\",\n",
-    "    },\n",
-    "    hover_data=[\"identifier\"],\n",
-    "    # currently does not work:\n",
-    "    # color_discrete_map={False: \"#2166AC\", True: \"#B2182B\"},  # Blue  # Red\n",
-    "    color_discrete_sequence=[\"red\", \"blue\"],\n",
-    "    opacity=1,\n",
-    "    marker_line_width=1,\n",
-    "    marker_line_color=\"darkgray\",\n",
-    "    width=800,\n",
-    "    height=600,\n",
-    ")\n",
-    "scatter_plot_adv"
+    "vuecore.interactive.get_differential_regulation_plot(\n",
+    "    data=anova,\n",
+    ")"
    ]
   },
   {

docs/examples_single_analysis/diff_regulation_anova_ttest_two_groups.py

@@ -34,7 +34,7 @@
 # %% tags=["hide-input"]
 import dsp_pandas
 import pandas as pd
-import vuecore.plots.basic.scatter
+import vuecore.interactive
 
 import acore.differential_regulation as ad
 
@@ -167,31 +167,10 @@
 #   which is True for significant features and False for non-significant features, and
 #   is calculated based on the `padj` column and a significance threshold (default 0.05)
 
+
 # %%
-scatter_plot_adv = vuecore.plots.basic.scatter.create_scatter_plot(
-    data=anova.reset_index(),
-    x="log2FC",
-    y="-log10 pvalue",
-    color="rejected",
-    title="Simple Volcano Plot",
-    subtitle="Visualizing ANOVA results",
-    labels={
-        "log2FC": "Log2 Fold Change",
-        "-log10 pvalue": "-log10(p-value)",
-        "rejected": "FDR corrected Significant",
-        "identifier": "Protein Identifier",
-    },
-    hover_data=["identifier"],
-    # currently does not work:
-    # color_discrete_map={False: "#2166AC", True: "#B2182B"},  # Blue  # Red
-    color_discrete_sequence=["red", "blue"],
-    opacity=1,
-    marker_line_width=1,
-    marker_line_color="darkgray",
-    width=800,
-    height=600,
+vuecore.interactive.get_differential_regulation_plot(
+    data=anova,
 )
-scatter_plot_adv
-
 # %% [markdown]
 # Done.

docs/markdown_ref/acore.md

@@ -265,13 +265,13 @@
       * [`AncovaSchema.posthoc_comparison`](acore.types.md#acore.types.differential_analysis.AncovaSchema.posthoc_comparison)
       * [`AncovaSchema.t_statistics`](acore.types.md#acore.types.differential_analysis.AncovaSchema.t_statistics)
       * [`AncovaSchema.posthoc_pvalue`](acore.types.md#acore.types.differential_analysis.AncovaSchema.posthoc_pvalue)
+      * [`AncovaSchema.f_statistics`](acore.types.md#acore.types.differential_analysis.AncovaSchema.f_statistics)
+      * [`AncovaSchema.posthoc_padj`](acore.types.md#acore.types.differential_analysis.AncovaSchema.posthoc_padj)
       * [`AncovaSchema.posthoc_rejected`](acore.types.md#acore.types.differential_analysis.AncovaSchema.posthoc_rejected)
       * [`AncovaSchema.coef`](acore.types.md#acore.types.differential_analysis.AncovaSchema.coef)
       * [`AncovaSchema.std_err`](acore.types.md#acore.types.differential_analysis.AncovaSchema.std_err)
       * [`AncovaSchema.conf_int_low`](acore.types.md#acore.types.differential_analysis.AncovaSchema.conf_int_low)
       * [`AncovaSchema.conf_int_upp`](acore.types.md#acore.types.differential_analysis.AncovaSchema.conf_int_upp)
-      * [`AncovaSchema.f_statistics`](acore.types.md#acore.types.differential_analysis.AncovaSchema.f_statistics)
-      * [`AncovaSchema.posthoc_padj`](acore.types.md#acore.types.differential_analysis.AncovaSchema.posthoc_padj)
       * [`AncovaSchema.Config`](acore.types.md#acore.types.differential_analysis.AncovaSchema.Config)
       * [`AncovaSchema.build_schema_()`](acore.types.md#acore.types.differential_analysis.AncovaSchema.build_schema_)
       * [`AncovaSchema.empty()`](acore.types.md#acore.types.differential_analysis.AncovaSchema.empty)

docs/markdown_ref/acore.types.md

@@ -27,7 +27,7 @@ containing NaN values.
 
 Bases: [`DataFrameModel`](https://pandera.readthedocs.io/en/stable/reference/generated/pandera.api.pandas.model.DataFrameModel.html#pandera.api.pandas.model.DataFrameModel)
 
-Schema for the enrichment analysis results DataFrame.
+Schema for the differential regulation analysis results DataFrame.
 
 #### group1 *: [str](https://docs.python.org/3/builtins/stdtypes.html#str)* *= 'group1'*
 
@@ -527,14 +527,18 @@ Validate a DataFrame based on the schema specification.
 
 Bases: [`DataFrameModel`](https://pandera.readthedocs.io/en/stable/reference/generated/pandera.api.pandas.model.DataFrameModel.html#pandera.api.pandas.model.DataFrameModel)
 
-Schema for the enrichment analysis results DataFrame.
+Schema for the differential regulation analysis results DataFrame.
 
 #### posthoc_comparison *: [str](https://docs.python.org/3/builtins/stdtypes.html#str)* *= 'posthoc comparison'*
 
 #### t_statistics *: [float](https://docs.python.org/3/builtins/functions.html#float)* *= 'posthoc T-Statistics'*
 
 #### posthoc_pvalue *: [float](https://docs.python.org/3/builtins/functions.html#float)* *= 'posthoc pvalue'*
 
+#### f_statistics *: [float](https://docs.python.org/3/builtins/functions.html#float)* *= 'F-statistics'*
+
+#### posthoc_padj *: [float](https://docs.python.org/3/builtins/functions.html#float)* *= 'posthoc pvalue adj'*
+
 #### posthoc_rejected *: [bool](https://docs.python.org/3/builtins/functions.html#bool)* *= 'posthoc rejected'*
 
 #### coef *: [float](https://docs.python.org/3/builtins/functions.html#float)* *= 'coef'*
@@ -545,10 +549,6 @@ Schema for the enrichment analysis results DataFrame.
 
 #### conf_int_upp *: [float](https://docs.python.org/3/builtins/functions.html#float)* *= 'Conf. Int. Upp.'*
 
-#### f_statistics *: [float](https://docs.python.org/3/builtins/functions.html#float)* *= 'F-statistics'*
-
-#### posthoc_padj *: [float](https://docs.python.org/3/builtins/functions.html#float)* *= 'posthoc pvalue adj'*
-
 #### *class* Config
 
 Bases: [`BaseConfig`](https://pandera.readthedocs.io/en/stable/reference/generated/pandera.api.pandas.model_config.BaseConfig.html#pandera.api.pandas.model_config.BaseConfig)

pyproject.toml

@@ -55,7 +55,7 @@ docs = [
   "sphinx-copybutton",
   "sphinx-llms-txt",
   # Multi-Omics-Analysis group package for visualisation of results in the documentation
-  "vuecore",
+  "vuecore>=0.3.0",
 ]
 dev = [
   "black[jupyter]",

src/acore/types/differential_analysis.py

@@ -3,7 +3,7 @@
 
 class AnovaSchema(DataFrameModel):
     """
-    Schema for the enrichment analysis results DataFrame.
+    Schema for the differential regulation analysis results DataFrame.
     """
 
     group1: str = Field(nullable=False)
@@ -57,16 +57,18 @@ class AnovaSchemaMultiGroup(AnovaSchema):
 
 class AncovaSchema(DataFrameModel):
     """
-    Schema for the enrichment analysis results DataFrame.
+    Schema for the differential regulation analysis results DataFrame.
     """
 
+    # same as in AnovaSchemaMultiGroup
     posthoc_comparison: str = Field(alias="posthoc comparison", nullable=False)
     t_statistics: float = Field(alias="posthoc T-Statistics")
     posthoc_pvalue: float = Field(alias="posthoc pvalue")
+    f_statistics: float = Field(alias="F-statistics")
+    posthoc_padj: float = Field(alias="posthoc pvalue adj", ge=0, le=1)
     posthoc_rejected: bool = Field(alias="posthoc rejected", nullable=False)
+
     coef: float = Field()
     std_err: float = Field(alias="std err")
     conf_int_low: float = Field(alias="Conf. Int. Low")
     conf_int_upp: float = Field(alias="Conf. Int. Upp.")
-    f_statistics: float = Field(alias="F-statistics")
-    posthoc_padj: float = Field(alias="posthoc pvalue adj", ge=0, le=1)