Merge pull request #5 from cobioda/bego

Bego

README.md

@@ -7,7 +7,7 @@
 [link-tests]: https://github.com/bfxomics/scispy/actions/workflows/test.yml
 [badge-docs]: https://img.shields.io/readthedocs/scispy
 
-scispy is a python package for in-situ spatial-omics datasets analysis, mainly developped for vizgen merscope,
+scispy is a pthon package for in-situ spatial-omics datasets analysis, mainly developped for vizgen merscope,
 scispy is build on top of spatialdata and spatialdata-io and spatialdata-plot librairies which can handle for
 Nanostring (cosmx) and 10xGenomics (Xenium) experiments.
 

docs/api.md

@@ -14,6 +14,8 @@
     :toctree: generated
 
     io.load_merscope
+    io.load_xenium
+    io.load_cosmx
 ```
 
 ## Preprocessing
@@ -27,6 +29,7 @@
 
     pp.run_scanpy
     pp.scvi_annotate
+    pp.sync_shape
 ```
 
 ## Tools
@@ -39,10 +42,14 @@
     :toctree: generated
 
     tl.add_to_shapes
+    tl.add_shapes_from_hdf5
     tl.add_to_points
     tl.get_sdata_polygon
-    tl.prep_pseudobulk
     tl.run_pseudobulk
+    tl.sdata_rotate
+    tl.sdata_querybox
+    tl.scis_prop
+    tl.shapes_of_cell_type
 ```
 
 ## Plotting
@@ -54,9 +61,10 @@
 .. autosummary::
     :toctree: generated
 
+    pl.plot_qc
+    pl.plot_sdata
+    pl.plot_multi_sdata
     pl.plot_shapes
     pl.plot_shape_along_axis
-    pl.plot_qc
     pl.plot_per_groups
-    pl.get_palette
 ```