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fix: Move NA values to end of table #124

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merged 7 commits into from
Oct 18, 2024
Merged

fix: Move NA values to end of table #124

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fb9239a
fix: Move NA values to end of table
fxwiegand Oct 16, 2024
f594b15
Update compare_diffexp.py
fxwiegand Oct 16, 2024
dca9161
Update compare_diffexp.py with dbg prints
fxwiegand Oct 16, 2024
69ef4d2
Update compare_diffexp.py
fxwiegand Oct 17, 2024
4776153
Update compare_diffexp.py
fxwiegand Oct 17, 2024
5f8dc17
refactor: Make meta comparison use proper logs
fxwiegand Oct 17, 2024
58d7cd5
Update compare_diffexp.py
fxwiegand Oct 17, 2024
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6 changes: 3 additions & 3 deletions workflow/rules/meta_comparisons.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ rule meta_compare_diffexp:
"results/tables/diffexp/meta_compare_{meta_comp}.tsv",
"results/meta_comparison/diffexp/{meta_comp}.json",
log:
notebook="logs/meta_compare_diffexp/{meta_comp}.ipynb",
"logs/meta_compare_diffexp/{meta_comp}.log",
params:
labels=lookup(
dpath="meta_comparisons/comparisons/{meta_comp}/items",
Expand Down Expand Up @@ -42,7 +42,7 @@ rule meta_compare_enrichment:
"results/tables/go_terms/meta_compare_{meta_comp}.tsv",
"results/meta_comparison/go_terms/{meta_comp}.json",
log:
notebook="logs/meta_compare_enrichment/{meta_comp}.ipynb",
"logs/meta_compare_enrichment/{meta_comp}.log",
params:
labels=lookup(
dpath="meta_comparisons/comparisons/{meta_comp}/items",
Expand All @@ -67,7 +67,7 @@ rule meta_compare_pathways:
"results/tables/pathways/meta_compare_{meta_comp}.tsv",
"results/meta_comparison/pathways/{meta_comp}.json",
log:
notebook="logs/meta_compare_pathways/{meta_comp}.ipynb",
"logs/meta_compare_pathways/{meta_comp}.log",
params:
labels=lookup(
dpath="meta_comparisons/comparisons/{meta_comp}/items",
Expand Down
10 changes: 9 additions & 1 deletion workflow/scripts/compare_diffexp.py
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Expand Up @@ -50,7 +50,15 @@ def prepare(df):
combined.with_columns(
(-pl.col("pval_min").log(base=10) * pl.col("difference")).alias("pi_value")
)
.sort(pl.col("pi_value").abs(), descending=True)
.with_columns(
pl.col("pi_value").fill_nan(None),
pl.col("difference").fill_nan(None),
)
Comment on lines +53 to +56
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This seems convoluted, but at least it's well documented:
https://docs.pola.rs/user-guide/expressions/missing-data/#notanumber-or-nan-values

.sort(
pl.col("pi_value").abs(),
descending=True,
nulls_last=True,
)
.select(
pl.col(
"ext_gene",
Expand Down
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