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Add linear model results from concat plates #40

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Mar 21, 2024
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Add linear model results from concat plates #40

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076f62d
add linear model results from concat plates
jenna-tomkinson Mar 18, 2024
46efbd7
update documentation
jenna-tomkinson Mar 18, 2024
d4d9362
update code and documentation
jenna-tomkinson Mar 21, 2024
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11 changes: 5 additions & 6 deletions 4.analyze_data/notebooks/linear_model/0.linear_model_coeff.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,11 @@
"outputs": [],
"source": [
"import pathlib\n",
"import pandas as pd\n",
"\n",
"from sklearn.linear_model import LinearRegression\n",
"\n",
"import pandas as pd\n",
"from pycytominer import feature_select\n",
"from pycytominer.cyto_utils import infer_cp_features\n"
"from pycytominer.cyto_utils import infer_cp_features\n",
"from sklearn.linear_model import LinearRegression"
]
},
{
Expand Down Expand Up @@ -347,7 +346,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Set up the dummy matrix between null and WT cell types\n"
"## Set up the binary matrix between Null and WT cell types\n"
]
},
{
Expand Down Expand Up @@ -442,7 +441,7 @@
"variables = [\"Metadata_number_of_singlecells\"]\n",
"X = cp_df.loc[:, variables]\n",
"\n",
"# Add dummy matrix of categorical genotypes\n",
"# Add binary matrix of categorical genotypes\n",
"genotype_x = pd.get_dummies(data=cp_df.Metadata_genotype)\n",
"\n",
"X = pd.concat([X, genotype_x], axis=1)\n",
Expand Down
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