fixed merge conflict

docs/api/index.md

@@ -1,7 +1,5 @@
 # API
 
-Import CREsted as:
-
 ```
 import crested
 ```
@@ -11,7 +9,7 @@ import crested
 
 io
 preprocessing
-tools
-plotting
+tools/index.md
+plotting/index.md
 logging
 ```

docs/api/io.md

@@ -4,15 +4,13 @@ Importing of topics bed files (outputs from [pycistopic](https://pycistopic.read
 Importing of bigwigs files and consensus region bed files into Anndata format for peak regression or classification.
 
 ```{eval-rst}
-.. module:: crested
+.. currentmodule:: crested
 ```
 
 ```{eval-rst}
-.. currentmodule:: crested
-
 .. autosummary::
     :toctree: _autosummary
 
     import_bigwigs
-    import_topics
+    import_beds
 ```

docs/api/logging.md

@@ -3,12 +3,10 @@
 Helper functions for logging during use of package.
 
 ```{eval-rst}
-.. module:: crested
+.. currentmodule:: crested
 ```
 
 ```{eval-rst}
-.. currentmodule:: crested
-
 .. autosummary::
     :toctree: _autosummary
 

docs/api/plotting/bar.md

@@ -0,0 +1,16 @@
+# Bar `pl.bar`
+
+Bar plots to inspect per region ground truths and compare them to their predictions.
+
+```{eval-rst}
+.. currentmodule:: crested.pl.bar
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: _autosummary
+
+    region
+    region_predictions
+    normalization_weights
+```

docs/api/plotting/heatmap.md

@@ -0,0 +1,15 @@
+# Heatmap `pl.heatmap`
+
+Investigate autocorrelation between classes and between ground truths and predictions using heatmaps.
+
+```{eval-rst}
+.. currentmodule:: crested.pl.heatmap
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: _autosummary
+
+    correlations_self
+    correlations_predictions
+```

docs/api/plotting/hist.md

@@ -0,0 +1,14 @@
+# Hist  `pl.hist`
+
+Plots for inspecting distributions of ground truth and predictions?
+
+```{eval-rst}
+.. currentmodule:: crested.pl.hist
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: _autosummary
+
+    distribution
+```

docs/api/plotting/index.md

@@ -0,0 +1,66 @@
+# Plotting: `pl`
+
+Plotting description
+
+```{eval-rst}
+.. currentmodule:: crested.pl
+```
+
+```{toctree}
+:maxdepth: 2
+:hidden:
+
+patterns
+bar
+hist
+heatmap
+scatter
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: _autosummary
+
+    render_plot
+```
+
+## Patterns: Contribution scores and Modisco results
+
+```{eval-rst}
+.. autosummary::
+    patterns.contribution_scores
+    patterns.modisco_results
+```
+
+## Bar plots
+
+```{eval-rst}
+.. autosummary::
+    bar.region
+    bar.region_predictions
+    bar.normalization_weights
+```
+
+## Distribution plots
+
+```{eval-rst}
+.. autosummary::
+    hist.distribution
+```
+
+## Heatmap
+
+Correlations
+
+```{eval-rst}
+.. autosummary::
+    heatmap.correlations_self
+    heatmap.correlations_predictions
+```
+
+## Scatter plots
+
+```{eval-rst}
+.. autosummary::
+    scatter.class_density
+```

docs/api/plotting/patterns.md

@@ -0,0 +1,15 @@
+# Patterns `pl.patterns`
+
+Plot contribution scores and analyze them using tfmodisco.
+
+```{eval-rst}
+.. currentmodule:: crested.pl.patterns
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: _autosummary
+
+    contribution_scores
+    modisco_results
+```

docs/api/plotting/scatter.md

@@ -0,0 +1,14 @@
+# Scatter `pl.scatter`
+
+Useful scatter plots.
+
+```{eval-rst}
+.. currentmodule:: crested.pl.scatter
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: _autosummary
+
+    class_density
+```

docs/api/preprocessing.md

@@ -3,16 +3,12 @@
 Preparing Anndata object for CREsted training/evaluations.
 
 ```{eval-rst}
-.. module:: crested.pp
-```
-
-```{eval-rst}
-.. currentmodule:: crested
+.. currentmodule:: crested.pp
 
 .. autosummary::
     :toctree: _autosummary
 
-    pp.train_val_test_split
-    pp.filter_regions_on_specificity
-    pp.normalize_peaks
+    train_val_test_split
+    filter_regions_on_specificity
+    normalize_peaks
 ```

docs/api/tools/data.md

@@ -0,0 +1,17 @@
+# Data `tl.data`
+
+Utility functions to prepare data for training and evaluation.  
+Generally, `tl.data.AnnDataModule` is the only one that should be called directly by the user. 
+
+```{eval-rst}
+.. currentmodule:: crested.tl.data
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: _autosummary
+
+    AnnDataModule
+    AnnDataLoader
+    AnnDataset
+```