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leehartleehart
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Rename plot_genes() labels param to gene_labelset everywhere
1 parent ed16b06 commit f1b1b35

10 files changed

Lines changed: 32 additions & 32 deletions

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‎malariagen_data/anoph/cnv_data.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -752,7 +752,7 @@ def plot_cnv_hmm_coverage(
752752
show: gplt_params.show = True,
753753
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
754754
gene_labels: Optional[gplt_params.gene_labels] = None,
755-
labels: Optional[gplt_params.labels] = None,
755+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
756756
) -> gplt_params.figure:
757757
debug = self._log.debug
758758

@@ -785,7 +785,7 @@ def plot_cnv_hmm_coverage(
785785
show=False,
786786
output_backend=output_backend,
787787
gene_labels=gene_labels,
788-
labels=labels,
788+
gene_labelset=gene_labelset,
789789
)
790790

791791
debug("combine plots into a single figure")
@@ -965,7 +965,7 @@ def plot_cnv_hmm_heatmap(
965965
genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
966966
show: gplt_params.show = True,
967967
gene_labels: Optional[gplt_params.gene_labels] = None,
968-
labels: Optional[gplt_params.labels] = None,
968+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
969969
) -> gplt_params.figure:
970970
debug = self._log.debug
971971

@@ -996,7 +996,7 @@ def plot_cnv_hmm_heatmap(
996996
x_range=fig1.x_range,
997997
show=False,
998998
gene_labels=gene_labels,
999-
labels=labels,
999+
gene_labelset=gene_labelset,
10001000
)
10011001

10021002
debug("combine plots into a single figure")

‎malariagen_data/anoph/fst.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -294,7 +294,7 @@ def plot_fst_gwss(
294294
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
295295
clip_min: fst_params.clip_min = 0.0,
296296
gene_labels: Optional[gplt_params.gene_labels] = None,
297-
labels: Optional[gplt_params.labels] = None,
297+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
298298
) -> gplt_params.figure:
299299
# gwss track
300300
fig1 = self.plot_fst_gwss_track(
@@ -330,7 +330,7 @@ def plot_fst_gwss(
330330
show=False,
331331
output_backend=output_backend,
332332
gene_labels=gene_labels,
333-
labels=labels,
333+
gene_labelset=gene_labelset,
334334
)
335335

336336
# combine plots into a single figure

‎malariagen_data/anoph/g123.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -439,7 +439,7 @@ def plot_g123_gwss(
439439
inline_array: base_params.inline_array = base_params.inline_array_default,
440440
chunks: base_params.chunks = base_params.native_chunks,
441441
gene_labels: Optional[gplt_params.gene_labels] = None,
442-
labels: Optional[gplt_params.labels] = None,
442+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
443443
) -> gplt_params.figure:
444444
# gwss track
445445
fig1 = self.plot_g123_gwss_track(
@@ -475,7 +475,7 @@ def plot_g123_gwss(
475475
show=False,
476476
output_backend=output_backend,
477477
gene_labels=gene_labels,
478-
labels=labels,
478+
gene_labelset=gene_labelset,
479479
)
480480

481481
# combine plots into a single figure

‎malariagen_data/anoph/genome_features.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -334,7 +334,7 @@ def plot_genes(
334334
title: Optional[gplt_params.title] = None,
335335
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
336336
gene_labels: Optional[gplt_params.gene_labels] = None,
337-
labels: Optional[gplt_params.labels] = None,
337+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
338338
) -> gplt_params.figure:
339339
debug = self._log.debug
340340

@@ -502,8 +502,8 @@ def plot_genes(
502502
fig.add_layout(gene_pointers_ls)
503503
fig.add_layout(gene_labels_ls)
504504

505-
if labels:
506-
fig.add_layout(labels)
505+
if gene_labelset:
506+
fig.add_layout(gene_labelset)
507507

508508
debug("tidy up the plot")
509509
fig.ygrid.visible = False

‎malariagen_data/anoph/gplt_params.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -126,7 +126,7 @@
126126
"A mapping of gene identifiers to custom labels, which will appear in the plot.",
127127
]
128128

129-
labels: TypeAlias = Annotated[
129+
gene_labelset: TypeAlias = Annotated[
130130
bokeh.models.LabelSet,
131131
"A LabelSet to use in the plot.",
132132
]

‎malariagen_data/anoph/h12.py‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -474,7 +474,7 @@ def plot_h12_gwss(
474474
chunks: base_params.chunks = base_params.native_chunks,
475475
inline_array: base_params.inline_array = base_params.inline_array_default,
476476
gene_labels: Optional[gplt_params.gene_labels] = None,
477-
labels: Optional[gplt_params.labels] = None,
477+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
478478
) -> gplt_params.figure:
479479
# Plot GWSS track.
480480
fig1 = self.plot_h12_gwss_track(
@@ -511,7 +511,7 @@ def plot_h12_gwss(
511511
show=False,
512512
output_backend=output_backend,
513513
gene_labels=gene_labels,
514-
labels=labels,
514+
gene_labelset=gene_labelset,
515515
)
516516

517517
# Combine plots into a single figure.
@@ -679,7 +679,7 @@ def plot_h12_gwss_multi_overlay(
679679
show: gplt_params.show = True,
680680
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
681681
gene_labels: Optional[gplt_params.gene_labels] = None,
682-
labels: Optional[gplt_params.labels] = None,
682+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
683683
) -> gplt_params.figure:
684684
# Plot GWSS track.
685685
fig1 = self.plot_h12_gwss_multi_overlay_track(
@@ -717,7 +717,7 @@ def plot_h12_gwss_multi_overlay(
717717
show=False,
718718
output_backend=output_backend,
719719
gene_labels=gene_labels,
720-
labels=labels,
720+
gene_labelset=gene_labelset,
721721
)
722722

723723
# Combine plots into a single figure.
@@ -764,7 +764,7 @@ def plot_h12_gwss_multi_panel(
764764
show: gplt_params.show = True,
765765
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
766766
gene_labels: Optional[gplt_params.gene_labels] = None,
767-
labels: Optional[gplt_params.labels] = None,
767+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
768768
) -> gplt_params.figure:
769769
cohort_queries = self._setup_cohort_queries(
770770
cohorts=cohorts,
@@ -818,7 +818,7 @@ def plot_h12_gwss_multi_panel(
818818
show=False,
819819
output_backend=output_backend,
820820
gene_labels=gene_labels,
821-
labels=labels,
821+
gene_labelset=gene_labelset,
822822
)
823823

824824
figs.append(fig2)

‎malariagen_data/anoph/h1x.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -306,7 +306,7 @@ def plot_h1x_gwss(
306306
chunks: base_params.chunks = base_params.native_chunks,
307307
inline_array: base_params.inline_array = base_params.inline_array_default,
308308
gene_labels: Optional[gplt_params.gene_labels] = None,
309-
labels: Optional[gplt_params.labels] = None,
309+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
310310
) -> gplt_params.figure:
311311
# Plot GWSS track.
312312
fig1 = self.plot_h1x_gwss_track(
@@ -344,7 +344,7 @@ def plot_h1x_gwss(
344344
show=False,
345345
output_backend=output_backend,
346346
gene_labels=gene_labels,
347-
labels=labels,
347+
gene_labelset=gene_labelset,
348348
)
349349

350350
# Combine plots into a single figure.

‎malariagen_data/anoph/snp_data.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1306,7 +1306,7 @@ def plot_snps(
13061306
max_snps: int = 200_000,
13071307
show: gplt_params.show = True,
13081308
gene_labels: Optional[gplt_params.gene_labels] = None,
1309-
labels: Optional[gplt_params.labels] = None,
1309+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
13101310
) -> gplt_params.figure:
13111311
# Plot SNPs track.
13121312
fig1 = self.plot_snps_track(
@@ -1333,7 +1333,7 @@ def plot_snps(
13331333
x_range=fig1.x_range,
13341334
show=False,
13351335
gene_labels=gene_labels,
1336-
labels=labels,
1336+
gene_labelset=gene_labelset,
13371337
)
13381338

13391339
# Layout tracks in a grid.

‎malariagen_data/anopheles.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -430,7 +430,7 @@ def plot_heterozygosity(
430430
chunks: base_params.chunks = base_params.native_chunks,
431431
inline_array: base_params.inline_array = base_params.inline_array_default,
432432
gene_labels: Optional[gplt_params.gene_labels] = None,
433-
labels: Optional[gplt_params.labels] = None,
433+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
434434
) -> gplt_params.figure:
435435
debug = self._log.debug
436436

@@ -492,7 +492,7 @@ def plot_heterozygosity(
492492
show=False,
493493
output_backend=output_backend,
494494
gene_labels=gene_labels,
495-
labels=labels,
495+
gene_labelset=gene_labelset,
496496
)
497497
figs.append(fig_genes)
498498

@@ -729,7 +729,7 @@ def plot_roh(
729729
chunks: base_params.chunks = base_params.native_chunks,
730730
inline_array: base_params.inline_array = base_params.inline_array_default,
731731
gene_labels: Optional[gplt_params.gene_labels] = None,
732-
labels: Optional[gplt_params.labels] = None,
732+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
733733
) -> gplt_params.figure:
734734
debug = self._log.debug
735735

@@ -803,7 +803,7 @@ def plot_roh(
803803
show=False,
804804
output_backend=output_backend,
805805
gene_labels=gene_labels,
806-
labels=labels,
806+
gene_labelset=gene_labelset,
807807
)
808808
figs.append(fig_genes)
809809

@@ -2297,7 +2297,7 @@ def plot_xpehh_gwss(
22972297
chunks: base_params.chunks = base_params.native_chunks,
22982298
inline_array: base_params.inline_array = base_params.inline_array_default,
22992299
gene_labels: Optional[gplt_params.gene_labels] = None,
2300-
labels: Optional[gplt_params.labels] = None,
2300+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
23012301
) -> gplt_params.figure:
23022302
# gwss track
23032303
fig1 = self.plot_xpehh_gwss_track(
@@ -2343,7 +2343,7 @@ def plot_xpehh_gwss(
23432343
show=False,
23442344
output_backend=output_backend,
23452345
gene_labels=gene_labels,
2346-
labels=labels,
2346+
gene_labelset=gene_labelset,
23472347
)
23482348

23492349
# combine plots into a single figure
@@ -2402,7 +2402,7 @@ def plot_ihs_gwss(
24022402
chunks: base_params.chunks = base_params.native_chunks,
24032403
inline_array: base_params.inline_array = base_params.inline_array_default,
24042404
gene_labels: Optional[gplt_params.gene_labels] = None,
2405-
labels: Optional[gplt_params.labels] = None,
2405+
gene_labelset: Optional[gplt_params.gene_labelset] = None,
24062406
) -> gplt_params.figure:
24072407
# gwss track
24082408
fig1 = self.plot_ihs_gwss_track(
@@ -2450,7 +2450,7 @@ def plot_ihs_gwss(
24502450
show=False,
24512451
output_backend=output_backend,
24522452
gene_labels=gene_labels,
2453-
labels=labels,
2453+
gene_labelset=gene_labelset,
24542454
)
24552455

24562456
# combine plots into a single figure

‎notebooks/plot_genes.ipynb‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -272,7 +272,7 @@
272272
" ]\n",
273273
")\n",
274274
"data_as_cds = bokeh.models.ColumnDataSource(data)\n",
275-
"labels = bokeh.models.LabelSet(\n",
275+
"gene_labelset = bokeh.models.LabelSet(\n",
276276
" source=data_as_cds,\n",
277277
" x='pos',\n",
278278
" y='y',\n",
@@ -285,7 +285,7 @@
285285
"\n",
286286
"ag3.plot_genes(\n",
287287
" region=\"2R\",\n",
288-
" labels=labels,\n",
288+
" gene_labelset=gene_labelset,\n",
289289
" height=200,\n",
290290
")"
291291
]

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