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leehartleehart
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Support gene_labels, labels params where plot_genes() is used
1 parent c314ed4 commit 3d4f7fc

7 files changed

Lines changed: 52 additions & 0 deletions

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‎malariagen_data/anoph/cnv_data.py‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -751,6 +751,8 @@ def plot_cnv_hmm_coverage(
751751
line_kwargs: Optional[gplt_params.line_kwargs] = None,
752752
show: gplt_params.show = True,
753753
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
754+
gene_labels: Optional[gplt_params.gene_labels] = None,
755+
labels: Optional[gplt_params.labels] = None,
754756
) -> gplt_params.figure:
755757
debug = self._log.debug
756758

@@ -782,6 +784,8 @@ def plot_cnv_hmm_coverage(
782784
x_range=fig1.x_range,
783785
show=False,
784786
output_backend=output_backend,
787+
gene_labels=gene_labels,
788+
labels=labels,
785789
)
786790

787791
debug("combine plots into a single figure")
@@ -960,6 +964,8 @@ def plot_cnv_hmm_heatmap(
960964
track_height: Optional[gplt_params.track_height] = None,
961965
genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
962966
show: gplt_params.show = True,
967+
gene_labels: Optional[gplt_params.gene_labels] = None,
968+
labels: Optional[gplt_params.labels] = None,
963969
) -> gplt_params.figure:
964970
debug = self._log.debug
965971

@@ -989,6 +995,8 @@ def plot_cnv_hmm_heatmap(
989995
height=genes_height,
990996
x_range=fig1.x_range,
991997
show=False,
998+
gene_labels=gene_labels,
999+
labels=labels,
9921000
)
9931001

9941002
debug("combine plots into a single figure")

‎malariagen_data/anoph/fst.py‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -293,6 +293,8 @@ def plot_fst_gwss(
293293
show: gplt_params.show = True,
294294
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
295295
clip_min: fst_params.clip_min = 0.0,
296+
gene_labels: Optional[gplt_params.gene_labels] = None,
297+
labels: Optional[gplt_params.labels] = None,
296298
) -> gplt_params.figure:
297299
# gwss track
298300
fig1 = self.plot_fst_gwss_track(
@@ -327,6 +329,8 @@ def plot_fst_gwss(
327329
x_range=fig1.x_range,
328330
show=False,
329331
output_backend=output_backend,
332+
gene_labels=gene_labels,
333+
labels=labels,
330334
)
331335

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# combine plots into a single figure

‎malariagen_data/anoph/g123.py‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -438,6 +438,8 @@ def plot_g123_gwss(
438438
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
439439
inline_array: base_params.inline_array = base_params.inline_array_default,
440440
chunks: base_params.chunks = base_params.native_chunks,
441+
gene_labels: Optional[gplt_params.gene_labels] = None,
442+
labels: Optional[gplt_params.labels] = None,
441443
) -> gplt_params.figure:
442444
# gwss track
443445
fig1 = self.plot_g123_gwss_track(
@@ -472,6 +474,8 @@ def plot_g123_gwss(
472474
x_range=fig1.x_range,
473475
show=False,
474476
output_backend=output_backend,
477+
gene_labels=gene_labels,
478+
labels=labels,
475479
)
476480

477481
# combine plots into a single figure

‎malariagen_data/anoph/h12.py‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -473,6 +473,8 @@ def plot_h12_gwss(
473473
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
474474
chunks: base_params.chunks = base_params.native_chunks,
475475
inline_array: base_params.inline_array = base_params.inline_array_default,
476+
gene_labels: Optional[gplt_params.gene_labels] = None,
477+
labels: Optional[gplt_params.labels] = None,
476478
) -> gplt_params.figure:
477479
# Plot GWSS track.
478480
fig1 = self.plot_h12_gwss_track(
@@ -508,6 +510,8 @@ def plot_h12_gwss(
508510
x_range=fig1.x_range,
509511
show=False,
510512
output_backend=output_backend,
513+
gene_labels=gene_labels,
514+
labels=labels,
511515
)
512516

513517
# Combine plots into a single figure.
@@ -674,6 +678,8 @@ def plot_h12_gwss_multi_overlay(
674678
genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
675679
show: gplt_params.show = True,
676680
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
681+
gene_labels: Optional[gplt_params.gene_labels] = None,
682+
labels: Optional[gplt_params.labels] = None,
677683
) -> gplt_params.figure:
678684
# Plot GWSS track.
679685
fig1 = self.plot_h12_gwss_multi_overlay_track(
@@ -710,6 +716,8 @@ def plot_h12_gwss_multi_overlay(
710716
x_range=fig1.x_range,
711717
show=False,
712718
output_backend=output_backend,
719+
gene_labels=gene_labels,
720+
labels=labels,
713721
)
714722

715723
# Combine plots into a single figure.
@@ -755,6 +763,8 @@ def plot_h12_gwss_multi_panel(
755763
genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
756764
show: gplt_params.show = True,
757765
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
766+
gene_labels: Optional[gplt_params.gene_labels] = None,
767+
labels: Optional[gplt_params.labels] = None,
758768
) -> gplt_params.figure:
759769
cohort_queries = self._setup_cohort_queries(
760770
cohorts=cohorts,
@@ -807,6 +817,8 @@ def plot_h12_gwss_multi_panel(
807817
x_range=figs[0].x_range,
808818
show=False,
809819
output_backend=output_backend,
820+
gene_labels=gene_labels,
821+
labels=labels,
810822
)
811823

812824
figs.append(fig2)

‎malariagen_data/anoph/h1x.py‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -305,6 +305,8 @@ def plot_h1x_gwss(
305305
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
306306
chunks: base_params.chunks = base_params.native_chunks,
307307
inline_array: base_params.inline_array = base_params.inline_array_default,
308+
gene_labels: Optional[gplt_params.gene_labels] = None,
309+
labels: Optional[gplt_params.labels] = None,
308310
) -> gplt_params.figure:
309311
# Plot GWSS track.
310312
fig1 = self.plot_h1x_gwss_track(
@@ -341,6 +343,8 @@ def plot_h1x_gwss(
341343
x_range=fig1.x_range,
342344
show=False,
343345
output_backend=output_backend,
346+
gene_labels=gene_labels,
347+
labels=labels,
344348
)
345349

346350
# Combine plots into a single figure.

‎malariagen_data/anoph/snp_data.py‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1305,6 +1305,8 @@ def plot_snps(
13051305
genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
13061306
max_snps: int = 200_000,
13071307
show: gplt_params.show = True,
1308+
gene_labels: Optional[gplt_params.gene_labels] = None,
1309+
labels: Optional[gplt_params.labels] = None,
13081310
) -> gplt_params.figure:
13091311
# Plot SNPs track.
13101312
fig1 = self.plot_snps_track(
@@ -1330,6 +1332,8 @@ def plot_snps(
13301332
height=genes_height,
13311333
x_range=fig1.x_range,
13321334
show=False,
1335+
gene_labels=gene_labels,
1336+
labels=labels,
13331337
)
13341338

13351339
# Layout tracks in a grid.

‎malariagen_data/anopheles.py‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -429,6 +429,8 @@ def plot_heterozygosity(
429429
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
430430
chunks: base_params.chunks = base_params.native_chunks,
431431
inline_array: base_params.inline_array = base_params.inline_array_default,
432+
gene_labels: Optional[gplt_params.gene_labels] = None,
433+
labels: Optional[gplt_params.labels] = None,
432434
) -> gplt_params.figure:
433435
debug = self._log.debug
434436

@@ -489,6 +491,8 @@ def plot_heterozygosity(
489491
x_range=fig1.x_range,
490492
show=False,
491493
output_backend=output_backend,
494+
gene_labels=gene_labels,
495+
labels=labels,
492496
)
493497
figs.append(fig_genes)
494498

@@ -724,6 +728,8 @@ def plot_roh(
724728
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
725729
chunks: base_params.chunks = base_params.native_chunks,
726730
inline_array: base_params.inline_array = base_params.inline_array_default,
731+
gene_labels: Optional[gplt_params.gene_labels] = None,
732+
labels: Optional[gplt_params.labels] = None,
727733
) -> gplt_params.figure:
728734
debug = self._log.debug
729735

@@ -796,6 +802,8 @@ def plot_roh(
796802
x_range=fig_het.x_range,
797803
show=False,
798804
output_backend=output_backend,
805+
gene_labels=gene_labels,
806+
labels=labels,
799807
)
800808
figs.append(fig_genes)
801809

@@ -2283,6 +2291,8 @@ def plot_xpehh_gwss(
22832291
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
22842292
chunks: base_params.chunks = base_params.native_chunks,
22852293
inline_array: base_params.inline_array = base_params.inline_array_default,
2294+
gene_labels: Optional[gplt_params.gene_labels] = None,
2295+
labels: Optional[gplt_params.labels] = None,
22862296
) -> gplt_params.figure:
22872297
# gwss track
22882298
fig1 = self.plot_xpehh_gwss_track(
@@ -2327,6 +2337,8 @@ def plot_xpehh_gwss(
23272337
x_range=fig1.x_range,
23282338
show=False,
23292339
output_backend=output_backend,
2340+
gene_labels=gene_labels,
2341+
labels=labels,
23302342
)
23312343

23322344
# combine plots into a single figure
@@ -2384,6 +2396,8 @@ def plot_ihs_gwss(
23842396
output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
23852397
chunks: base_params.chunks = base_params.native_chunks,
23862398
inline_array: base_params.inline_array = base_params.inline_array_default,
2399+
gene_labels: Optional[gplt_params.gene_labels] = None,
2400+
labels: Optional[gplt_params.labels] = None,
23872401
) -> gplt_params.figure:
23882402
# gwss track
23892403
fig1 = self.plot_ihs_gwss_track(
@@ -2430,6 +2444,8 @@ def plot_ihs_gwss(
24302444
x_range=fig1.x_range,
24312445
show=False,
24322446
output_backend=output_backend,
2447+
gene_labels=gene_labels,
2448+
labels=labels,
24332449
)
24342450

24352451
# combine plots into a single figure

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