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Allow multiple SNP transcripts in plot_diplotype_clustering_advanced() #703

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Merged
merged 13 commits into from
Feb 6, 2025
Merged

Allow multiple SNP transcripts in plot_diplotype_clustering_advanced() #703

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34c24c8
Updated the notebook
jonbrenas Dec 12, 2024
75b4cc3
Better typing
jonbrenas Dec 12, 2024
6b9767d
More tests and some trimming of the hierarchy in anoph
jonbrenas Dec 13, 2024
a2c4275
Testing something
jonbrenas Dec 13, 2024
b74a0a8
Better typing, hopefully
jonbrenas Dec 13, 2024
832ba29
Removed the heterozygosity blcok
jonbrenas Dec 13, 2024
911010b
Another erroneous type
jonbrenas Dec 13, 2024
fbb1a39
Merge branch 'master' into 600-adding-option-for-multiple-transcripts…
jonbrenas Dec 13, 2024
7a8aaf6
Made snp_transcript polymorphic to avoid breaking the API
jonbrenas Dec 13, 2024
d57e8bc
Merge branch '600-adding-option-for-multiple-transcripts-to-diplotype…
jonbrenas Dec 13, 2024
4d0fac4
Better typing
jonbrenas Dec 13, 2024
7104cdb
Merge branch 'master' into 600-adding-option-for-multiple-transcripts…
jonbrenas Jan 2, 2025
450235b
Merge branch 'master' into 600-adding-option-for-multiple-transcripts…
jonbrenas Feb 5, 2025
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20 changes: 11 additions & 9 deletions malariagen_data/anoph/dipclust.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
from typing import Optional, Tuple
from typing import Optional, Tuple, Sequence

import allel # type: ignore
import numpy as np
Expand All @@ -23,14 +23,16 @@
cnv_params,
)
from .snp_frq import AnophelesSnpFrequencyAnalysis
from .cnv_data import AnophelesCnvData
from .cnv_frq import AnophelesCnvFrequencyAnalysis

AA_CHANGE_QUERY = (
"effect in ['NON_SYNONYMOUS_CODING', 'START_LOST', 'STOP_LOST', 'STOP_GAINED']"
)


class AnophelesDipClustAnalysis(AnophelesSnpFrequencyAnalysis, AnophelesCnvData):
class AnophelesDipClustAnalysis(
AnophelesCnvFrequencyAnalysis, AnophelesSnpFrequencyAnalysis
):
def __init__(
self,
**kwargs,
Expand Down Expand Up @@ -190,7 +192,7 @@ def plot_diplotype_clustering(
else:
return {
"figure": fig,
"dendro_sample_id_order": leaf_data["sample_id"].to_list(),
"dendro_sample_id_order": np.asarray(leaf_data["sample_id"].to_list()),
"n_snps": n_snps_used,
}

Expand Down Expand Up @@ -319,7 +321,7 @@ def _dipclust_het_bar_trace(
sample_sets: Optional[base_params.sample_sets],
sample_query: Optional[base_params.sample_query],
sample_query_options: Optional[base_params.sample_query_options],
site_mask: base_params.site_mask,
site_mask: Optional[base_params.site_mask],
cohort_size: Optional[base_params.cohort_size],
random_seed: base_params.random_seed,
color_continuous_scale: Optional[plotly_params.color_continuous_scale],
Expand Down Expand Up @@ -551,7 +553,7 @@ def _dipclust_concat_subplots(
summary="Perform diplotype clustering, annotated with heterozygosity, gene copy number and amino acid variants.",
parameters=dict(
heterozygosity="Plot heterozygosity track.",
snp_transcript="Plot amino acid variants for this transcript.",
snp_transcripts="Plot amino acid variants for these transcripts.",
cnv_region="Plot gene CNV calls for this region.",
snp_filter_min_maf="Filter amino acid variants with alternate allele frequency below this threshold.",
),
Expand All @@ -561,7 +563,7 @@ def plot_diplotype_clustering_advanced(
region: base_params.regions,
heterozygosity: bool = True,
heterozygosity_colorscale: plotly_params.color_continuous_scale = "Greys",
snp_transcript: Optional[base_params.transcript] = None,
snp_transcripts: Sequence[base_params.transcript] = [],
snp_colorscale: plotly_params.color_continuous_scale = "Greys",
snp_filter_min_maf: float = 0.05,
snp_query: Optional[base_params.snp_query] = AA_CHANGE_QUERY,
Expand Down Expand Up @@ -601,7 +603,7 @@ def plot_diplotype_clustering_advanced(
chunks: base_params.chunks = base_params.native_chunks,
inline_array: base_params.inline_array = base_params.inline_array_default,
):
if cohort_size and snp_transcript:
if cohort_size and snp_transcripts:
cohort_size = None
print(
"Cohort size is not supported with amino acid heatmap. Overriding cohort size to None."
Expand Down Expand Up @@ -682,7 +684,7 @@ def plot_diplotype_clustering_advanced(
figures.append(cnv_trace)
subplot_heights.append(cnv_row_height * n_cnv_genes)

if snp_transcript:
for snp_transcript in snp_transcripts:
snp_trace, n_snps_transcript = self._dipclust_snp_trace(
transcript=snp_transcript,
sample_sets=sample_sets,
Expand Down
9 changes: 0 additions & 9 deletions malariagen_data/anopheles.py
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Not clear why there are any changes to this file included in this PR?

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@jonbrenas jonbrenas Dec 13, 2024 •
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AnophelesDipClustAnalysis needs to inherit gene_cnv from AnophelesCnvFrequencyAnalysis (see comment below) which created a loop in the inheritance tree. Because AnophelesDipClustAnalysis is a subclass of AnophelesCnvFrequencyAnalysis and AnophelesSnpFrequencyAnalysis, when AnophelesDataResource inherits AnophelesDipClustAnalysis, it also inherits them so they don't need to be included in the list of inherited classes anymore.

Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,6 @@
import plotly.graph_objects as go # type: ignore
from numpydoc_decorator import doc # type: ignore

from malariagen_data.anoph.snp_frq import (
AnophelesSnpFrequencyAnalysis,
)

from .anoph.cnv_frq import AnophelesCnvFrequencyAnalysis

from .anoph import (
aim_params,
Expand All @@ -31,7 +26,6 @@
)
from .anoph.aim_data import AnophelesAimData
from .anoph.base import AnophelesBase
from .anoph.cnv_data import AnophelesCnvData
from .anoph.genome_features import AnophelesGenomeFeaturesData
from .anoph.genome_sequence import AnophelesGenomeSequenceData
from .anoph.hap_data import AnophelesHapData, hap_params
Expand Down Expand Up @@ -87,8 +81,6 @@ class AnophelesDataResource(
AnophelesH12Analysis,
AnophelesG123Analysis,
AnophelesFstAnalysis,
AnophelesCnvFrequencyAnalysis,
AnophelesSnpFrequencyAnalysis,
AnophelesHapFrequencyAnalysis,
AnophelesDistanceAnalysis,
AnophelesPca,
Expand All @@ -97,7 +89,6 @@ class AnophelesDataResource(
AnophelesAimData,
AnophelesHapData,
AnophelesSnpData,
AnophelesCnvData,
AnophelesSampleMetadata,
AnophelesGenomeFeaturesData,
AnophelesGenomeSequenceData,
Expand Down
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