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Issue 237, ensure ancestry plot only uses project QC, standardizing plots in QC report #273

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Issue 237, ensure ancestry plot only uses project QC, standardizing plots in QC report #273

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7e277b9
Add code mapping label to color in plot_*.py scripts
Apr 12, 2024
c99eea8
Revert "Add code mapping label to color in plot_*.py scripts"
Apr 12, 2024
9bdf8f8
Revert "fixup: Format Python code with Black"
Apr 12, 2024
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2 changes: 1 addition & 1 deletion src/cgr_gwas_qc/workflow/scripts/sample_concordance.py
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Expand Up @@ -186,7 +186,7 @@ def _discordant_logic(sr: pd.Series) -> bool:
]
):
# No metrics so ignore
# Issue 210: If someone is an expected replicates but has no PLINK, GRAF, or KING then these should be flagged as an discordant replicate (True). Before was returning False
# Issue 210: If someone is an expected replicates but has no PLINK, GRAF, or KING then these should be flagged as an discordant replicate (True). Before was returning False
return True

if pd.notna(sr.PLINK_is_ge_concordance):
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1 change: 0 additions & 1 deletion src/cgr_gwas_qc/workflow/scripts/sample_qc_table.py
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Expand Up @@ -437,7 +437,6 @@ def _read_intensity(file_name: Optional[Path], Sample_IDs: pd.Index) -> pd.Serie
.IdatIntensity
)


# TO-ADD: Add a parsing/summary function that returns a Series or DataFrame indexed by Sample_ID


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