🚑 fix compensation formula

README.md

@@ -18,7 +18,9 @@ Follow https://twitter.com/marenbuettner to learn about a first public release.
 
 For beta users: Read the [docs](https://pytometry.netlify.app).
 
-You can install `pytometry` via [pip](https://pip.pypa.io/) from [PyPI](PyPI):
+## Installation
+
+You can install `pytometry` via [pip](https://pip.pypa.io/) from [PyPI](https://pypi.org/):
 
 ```
 pip install pytometry

docs/index.md

@@ -1,6 +1,6 @@
 ```{include} ../README.md
 :start-line: 0
-:end-line: 17
+:end-line: 35
 ```
 
 ```{toctree}

docs/tutorials/quickstart.ipynb

@@ -78,6 +78,16 @@
     "pm.pl.plotdata(adata)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5fb73d4d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pm.pl.scatter_density(adata)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

pytometry/__init__.py

@@ -20,7 +20,7 @@
 
 """
 
-__version__ = "0.1.1"  # denote a pre-release for 0.1.0 with 0.1a1
+__version__ = "0.1.2"  # denote a pre-release for 0.1.0 with 0.1a1
 
 from . import plotting as pl
 from . import preprocessing as pp

pytometry/plotting/__init__.py

@@ -1 +1,2 @@
 from ._histogram import plotdata
+from ._scatter_density import scatter_density

pytometry/preprocessing/_process_data.py

@@ -171,9 +171,8 @@ def compensate(
     compens = compens.iloc[query_idx, query_idx]
     # sort compensation matrix by adata.var_names
     compens = compens.iloc[idx_sort, idx_sort]
-    X_comp = np.linalg.solve(compens, adata.X[:, ref_idx].T).T
+    X_comp = np.linalg.solve(compens.T, adata.X[:, ref_idx].T).T
     adata.X[:, ref_idx] = X_comp
-
     # check for nan values
     nan_val = np.isnan(adata.X[:, ref_idx]).sum()
     if nan_val > 0: