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fix: relative aggregation sample plot #412

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merged 12 commits into from
Jan 4, 2022
Merged

fix: relative aggregation sample plot #412

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f34d012
Changed plots occurence threshold to relative
AKBrueggemann Dec 8, 2021
5698894
fmt
AKBrueggemann Dec 8, 2021
7ad1ecf
Name changed: number of occurences in plot
AKBrueggemann Dec 8, 2021
8d9ada2
fmt
AKBrueggemann Dec 8, 2021
f1da47f
Merge 'master' into relative-aggregation-sample-pl
AKBrueggemann Dec 15, 2021
8e1f568
Changed threshold values for variant/lineage plots
AKBrueggemann Dec 15, 2021
46d6f75
Merge branch 'master' into relative-aggregation-sample-plot
AKBrueggemann Dec 16, 2021
ebff8ed
Changed way of thresholding lineages/variants
AKBrueggemann Jan 3, 2022
207f020
Merge branch 'relative-aggregation-sample-plot' of https://github.com…
AKBrueggemann Jan 3, 2022
b691c66
fmt
AKBrueggemann Jan 3, 2022
1442c01
Changed name for other occ. in plot
AKBrueggemann Jan 3, 2022
d45a9e5
Merge branch 'master' into relative-aggregation-sample-plot
thomasbtf Jan 4, 2022
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15 changes: 11 additions & 4 deletions workflow/scripts/plot-lineages-over-time.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,17 @@ def plot_lineages_over_time(sm_input, sm_output, dates, sm_output_table):
pangolin_calls["lineage_count"] = pd.Series()

# mask low occurrences
threshold = len(pangolin_calls) / 10
pangolin_calls.loc[pangolin_calls["lineage_count"] < threshold, "lineage"] = (
"other (<" + str(threshold) + " occ.)"
)
print(pangolin_calls["lineage"].value_counts())
df = pd.DataFrame(pangolin_calls["lineage"].value_counts())
df.sort_values(by=["lineage"])
if len(df.index) > 10:
pangolin_calls.loc[
~df.head(10).isin(pangolin_calls["lineage"]), "lineage"
] = "other occ."
else:
pangolin_calls.loc[
pangolin_calls["lineage_count"] < 0, "lineage"
] = "other occ."

pangolin_calls.rename(columns={"lineage": "Lineage", "date": "Date"}, inplace=True)

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14 changes: 10 additions & 4 deletions workflow/scripts/plot-variants-over-time.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,10 +84,16 @@ def plot_variants_over_time(sm_output, sm_output_table):
].transform(lambda s: s.count())

# mask low occurrences
threshold = len(calls) / 10
calls.loc[calls["total occurrence"] < threshold, "alteration"] = (
"other (<" + str(threshold) + " occ.)"
)
print(calls["alteration"].value_counts())
df = pd.DataFrame(calls["alteration"].value_counts())
df.sort_values(by=["alteration"])
if len(df.index) > 10:
# print(calls.loc[calls["alteration"].isin(df.head(10).index)])
calls.loc[
~calls["alteration"].isin(df.head(10).index), "alteration"
] = "other occ."
else:
calls.loc[calls["total occurrence"] < 0, "alteration"] = "other occ."

calls.rename(columns={"alteration": "Alteration", "date": "Date"}, inplace=True)

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