Skip to content

Commit 5a273d0

Browse files
sanjaynagisanjaynagi
committed
add support for multiple transcripts, lines
1 parent 36f6d51 commit 5a273d0

2 files changed

Lines changed: 136 additions & 45 deletions

File tree

‎malariagen_data/anoph/dipclust.py‎

Lines changed: 52 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -538,7 +538,7 @@ def _insert_dipclust_snp_trace(
538538
print(
539539
f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot."
540540
)
541-
return figures, subplot_heights
541+
return figures, subplot_heights, n_snps_transcript
542542

543543
@doc(
544544
summary=""""
@@ -679,8 +679,13 @@ def plot_diplotype_clustering_advanced(
679679
figures.append(cnv_trace)
680680
subplot_heights.append(cnv_row_height * n_cnv_genes)
681681

682+
n_snps_transcripts = []
682683
if isinstance(snp_transcript, str):
683-
figures, subplot_heights = self._insert_dipclust_snp_trace(
684+
(
685+
figures,
686+
subplot_heights,
687+
n_snps_transcript,
688+
) = self._insert_dipclust_snp_trace(
684689
transcript=snp_transcript,
685690
figures=figures,
686691
subplot_heights=subplot_heights,
@@ -696,9 +701,14 @@ def plot_diplotype_clustering_advanced(
696701
chunks=chunks,
697702
inline_array=inline_array,
698703
)
704+
n_snps_transcripts.append(n_snps_transcript)
699705
elif isinstance(snp_transcript, list):
700706
for st in snp_transcript:
701-
figures, subplot_heights = self._insert_dipclust_snp_trace(
707+
(
708+
figures,
709+
subplot_heights,
710+
n_snps_transcript,
711+
) = self._insert_dipclust_snp_trace(
702712
transcript=st,
703713
figures=figures,
704714
subplot_heights=subplot_heights,
@@ -714,6 +724,7 @@ def plot_diplotype_clustering_advanced(
714724
chunks=chunks,
715725
inline_array=inline_array,
716726
)
727+
n_snps_transcripts.append(n_snps_transcript)
717728

718729
# Calculate total height based on subplot heights, plus a fixed
719730
# additional component to allow for title, axes etc.
@@ -739,6 +750,44 @@ def plot_diplotype_clustering_advanced(
739750
legend=dict(itemsizing=legend_sizing, tracegroupgap=0),
740751
)
741752

753+
# add lines to aa plot - looks neater
754+
if snp_transcript:
755+
n_transcripts = (
756+
len(snp_transcript) if isinstance(snp_transcript, list) else 1
757+
)
758+
for i in range(n_transcripts):
759+
tx_idx = len(figures) - n_transcripts + i + 1
760+
if n_snps_transcripts[i] > 0:
761+
fig.add_hline(
762+
y=-0.5, line_width=1, line_color="grey", row=tx_idx, col=1
763+
)
764+
for j in range(n_snps_transcripts[i]):
765+
fig.add_hline(
766+
y=j + 0.5,
767+
line_width=1,
768+
line_color="grey",
769+
row=tx_idx,
770+
col=1,
771+
)
772+
773+
fig.update_xaxes(
774+
showline=True,
775+
linecolor="grey",
776+
linewidth=1,
777+
row=tx_idx,
778+
col=1,
779+
mirror=True,
780+
)
781+
782+
fig.update_yaxes(
783+
showline=True,
784+
linecolor="grey",
785+
linewidth=1,
786+
row=tx_idx,
787+
col=1,
788+
mirror=True,
789+
)
790+
742791
if show:
743792
fig.show(renderer=renderer)
744793
return None

‎malariagen_data/anoph/hapclust.py‎

Lines changed: 84 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -468,22 +468,50 @@ def plot_haplotype_clustering_advanced(
468468
figures.append(snp_trace)
469469
subplot_heights.append(25)
470470

471-
figures, subplot_heights, df_haps = self._insert_hapclust_snp_trace(
472-
transcript=snp_transcript,
473-
snp_query=snp_query,
474-
figures=figures,
475-
subplot_heights=subplot_heights,
476-
sample_sets=sample_sets,
477-
sample_query=sample_query,
478-
analysis=analysis,
479-
dendro_sample_id_order=dendro_sample_id_order,
480-
snp_filter_min_maf=snp_filter_min_maf,
481-
snp_colorscale=snp_colorscale,
482-
snp_row_height=snp_row_height,
483-
chunks=chunks,
484-
inline_array=inline_array,
485-
)
486-
n_aa = df_haps.shape[0]
471+
n_snps_transcripts = []
472+
if isinstance(snp_transcript, str):
473+
(
474+
figures,
475+
subplot_heights,
476+
n_snps_transcript,
477+
) = self._insert_hapclust_snp_trace(
478+
transcript=snp_transcript,
479+
snp_query=snp_query,
480+
figures=figures,
481+
subplot_heights=subplot_heights,
482+
sample_sets=sample_sets,
483+
sample_query=sample_query,
484+
analysis=analysis,
485+
dendro_sample_id_order=dendro_sample_id_order,
486+
snp_filter_min_maf=snp_filter_min_maf,
487+
snp_colorscale=snp_colorscale,
488+
snp_row_height=snp_row_height,
489+
chunks=chunks,
490+
inline_array=inline_array,
491+
)
492+
n_snps_transcripts.append(n_snps_transcript)
493+
elif isinstance(snp_transcript, list):
494+
for st in snp_transcript:
495+
(
496+
figures,
497+
subplot_heights,
498+
n_snps_transcript,
499+
) = self._insert_hapclust_snp_trace(
500+
transcript=st,
501+
snp_query=snp_query,
502+
figures=figures,
503+
subplot_heights=subplot_heights,
504+
sample_sets=sample_sets,
505+
sample_query=sample_query,
506+
analysis=analysis,
507+
dendro_sample_id_order=dendro_sample_id_order,
508+
snp_filter_min_maf=snp_filter_min_maf,
509+
snp_colorscale=snp_colorscale,
510+
snp_row_height=snp_row_height,
511+
chunks=chunks,
512+
inline_array=inline_array,
513+
)
514+
n_snps_transcripts.append(n_snps_transcript)
487515

488516
# Calculate total height based on subplot heights, plus a fixed
489517
# additional component to allow for title, axes etc.
@@ -499,45 +527,57 @@ def plot_haplotype_clustering_advanced(
499527
n_snps=n_snps_cluster,
500528
)
501529

502-
fig["layout"]["yaxis"]["title"] = "Distance"
530+
fig["layout"]["yaxis"]["title"] = f"Distance ({distance_metric})"
503531
fig.update_layout(
504532
title_font=dict(
505533
size=title_font_size,
506534
),
507535
legend=dict(itemsizing=legend_sizing, tracegroupgap=0),
508536
)
509537

510-
if snp_transcript and n_aa > 0:
511-
# add lines to aa plot
512-
aa_idx = len(figures)
513-
fig.add_hline(y=-0.5, line_width=1, line_color="grey", row=aa_idx, col=1)
514-
for i in range(n_aa):
515-
fig.add_hline(
516-
y=i + 0.5, line_width=1, line_color="grey", row=aa_idx, col=1
538+
# add lines to aa plot - looks neater
539+
if snp_transcript:
540+
n_transcripts = (
541+
len(snp_transcript) if isinstance(snp_transcript, list) else 1
542+
)
543+
for i in range(n_transcripts):
544+
tx_idx = len(figures) - n_transcripts + i + 1
545+
if n_snps_transcripts[i] > 0:
546+
fig.add_hline(
547+
y=-0.5, line_width=1, line_color="grey", row=tx_idx, col=1
548+
)
549+
for j in range(n_snps_transcripts[i]):
550+
fig.add_hline(
551+
y=j + 0.5,
552+
line_width=1,
553+
line_color="grey",
554+
row=tx_idx,
555+
col=1,
556+
)
557+
558+
fig.update_xaxes(
559+
showline=True,
560+
linecolor="grey",
561+
linewidth=1,
562+
row=tx_idx,
563+
col=1,
564+
mirror=True,
517565
)
518566

519-
fig.update_xaxes(
520-
showline=True,
521-
linecolor="grey",
522-
linewidth=1,
523-
row=aa_idx,
524-
col=1,
525-
mirror=True,
526-
)
527-
fig.update_yaxes(
528-
showline=True,
529-
linecolor="grey",
530-
linewidth=1,
531-
row=aa_idx,
532-
col=1,
533-
mirror=True,
534-
)
567+
fig.update_yaxes(
568+
showline=True,
569+
linecolor="grey",
570+
linewidth=1,
571+
row=tx_idx,
572+
col=1,
573+
mirror=True,
574+
)
535575

536576
if show:
537577
fig.show(renderer=renderer)
538578
return None
539579
else:
540-
return fig, leaf_data, df_haps
580+
return fig, leaf_data
541581

542582
def transcript_haplotypes(
543583
self,
@@ -642,6 +682,8 @@ def _insert_hapclust_snp_trace(
642682
df_haps = df_haps.assign(af=lambda x: x.sum(axis=1) / x.shape[1])
643683
df_haps = df_haps.query("af > @snp_filter_min_maf").drop(columns="af")
644684

685+
n_snps_transcript = df_haps.shape[0]
686+
645687
if not df_haps.empty:
646688
snp_trace = go.Heatmap(
647689
z=df_haps.values,
@@ -660,7 +702,7 @@ def _insert_hapclust_snp_trace(
660702
print(
661703
f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot."
662704
)
663-
return figures, subplot_heights, df_haps
705+
return figures, subplot_heights, n_snps_transcript
664706

665707
def cut_dist_tree(
666708
self,

0 commit comments

Comments
 (0)