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Remove cytodataframe.show_report references #153

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Dec 15, 2024
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Remove cytodataframe.show_report references #153

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9c5d759
remove cytodataframe show_report references
d33bs Dec 10, 2024
0b340a0
linting and coverage badge
d33bs Dec 10, 2024
fdd0ca9
Delete cosmicqc_example_report.png
d33bs Dec 10, 2024
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11,538 changes: 5 additions & 11,533 deletions docs/src/examples/cosmicqc_in_a_nutshell.ipynb
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9 changes: 3 additions & 6 deletions docs/src/examples/cosmicqc_in_a_nutshell.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.16.2
# jupytext_version: 1.16.4
# kernelspec:
# display_name: Python 3 (ipykernel)
# language: python
Expand All @@ -20,6 +20,7 @@
import pathlib

import pandas as pd
from cytodataframe import CytoDataFrame

import cosmicqc

Expand All @@ -35,7 +36,7 @@
mask_context_dir = pathlib.Path(data_path).parent / "Plate_2_masks"

# create a cosmicqc CytoDataFrame (single-cell DataFrame)
scdf = cosmicqc.CytoDataFrame(
scdf = CytoDataFrame(
data=data_path,
data_context_dir=image_context_dir,
data_mask_context_dir=mask_context_dir,
Expand Down Expand Up @@ -75,10 +76,6 @@
labeled_scdf.iloc[:, -8:]
# -

# show histogram reports on the outliers and inliers
# for each threshold set in the new columns
labeled_scdf.show_report() # fmt: skip

# show cropped images through CytoDataFrame from the dataset to help analyze outliers
labeled_scdf.sort_values(by="cqc.large_nuclei.is_outlier", ascending=False)[
[
Expand Down
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