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🎨 improved split_signal #18

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Merged
mbuttner merged 2 commits into from
Aug 8, 2022
+7 −40
Merged

🎨 improved split_signal #18

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ce3c9fd
:art: improve split_signal
mbuttner Aug 8, 2022
d8e0f66
:memo: adjust pp notebook
mbuttner Aug 8, 2022
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41 changes: 3 additions & 38 deletions docs/tutorials/preprocessing.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -82,15 +82,6 @@
"We split the data matrix into the marker intensity part and the FSC/SSC part. Moreover, we move all height related features to the `.obs` part of the anndata file. Notably. the function `split_signal` checks if a feature name is either FSC/SSC or whether a name endswith `-A` for area related features and `-H` for height related features. "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"pm.pp.split_signal(adata)"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -111,33 +102,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Let us modify the feature column `signal_type` manually."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"adata.var[\"signal_type\"] = adata.var[\"signal_type\"].cat.add_categories([\"area\"])\n",
"adata.var[\"signal_type\"][3:] = \"area\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"adata.var"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Repeat to split the data matrix."
"We use the `channel` column of the `adata.var` data frame to split the matrix."
]
},
{
Expand All @@ -146,7 +111,7 @@
"metadata": {},
"outputs": [],
"source": [
"pm.pp.split_signal(adata)"
"pm.pp.split_signal(adata, var_key=\"channel\")"
]
},
{
Expand All @@ -162,7 +127,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"This time, we did not get the warning that all features are returned. Indeed, the data matrix was reduced by three features (`FSC-A`, `FSC-H` and `SSC-A`). "
"The data matrix was reduced by three features (`FSC-A`, `FSC-H` and `SSC-A`). "
]
},
{
Expand Down
6 changes: 4 additions & 2 deletions pytometry/preprocessing/_process_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ def create_comp_mat(spillmat: pd.DataFrame, relevant_data: str = "") -> pd.DataF

def find_indexes(
adata: AnnData,
var_key=None,
var_key: str = None,
key_added="signal_type",
data_type="facs",
inplace: bool = True,
Expand Down Expand Up @@ -94,7 +94,7 @@ def find_indexes(
f"{data_type} not recognized. Must be either 'facs' or "
" 'cytof'"
)
adata.var["signal_type"] = pd.Categorical(index_array)
adata.var[key_added] = pd.Categorical(index_array)
return None if inplace else adata


Expand Down Expand Up @@ -241,6 +241,8 @@ def split_signal(
# merge non-idx entries in data matrix with obs
non_cols = adata.var_names[non_idx].values
for idx, colname in enumerate(non_cols):
if colname == "":
colname = adata.var["channel"][non_idx[idx]]
adata.obs[colname] = adata.X[:, non_idx[idx]].copy()

# subset the anndata object
Expand Down