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Merge pull request #78 from anopheles-genomic-surveillance/reorder-se…
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…lection-alerts-06-03-24

reorder and rename selection alerts
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@sanjaynagi
sanjaynagi authored Mar 6, 2024
2 parents 3311277 + 40dbb6d commit c04a60d
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80 changes: 40 additions & 40 deletions docs/alert/vgsc.ipynb → docs/alert/SA-1-Vgsc.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -62,22 +62,7 @@
"id": "1f2288aa-fe3d-44c2-88be-aa897d9b4b49",
"metadata": {},
"source": [
"# *Vgsc*\n",
"\n",
"AGAP004707 (*Vgsc*)\n",
"\n",
"Mutations in this gene cause resistance to pyrethroid insecticides and DDT. The most common of these mutations is L995F, which is found across many insect taxa. In *Anopheles gambiae s.l*, we observe many distinct variants under selection, for example, L995F, L995S, and a haplotype containing both V402L and I1527T [(Clarkson *et al.,* 2021)](https://doi.org/10.1111/mec.15845). \n",
"\n",
"This form of resistance was first reported in *Anopheles gambiae* in 1998 [(Martinez-Torres *et al.,* 1998)](https://pubmed.ncbi.nlm.nih.gov/9535162/). Mutants at this locus are now found throughout sub-Saharan Africa. "
]
},
{
"cell_type": "markdown",
"id": "97da6cd4-0dc2-4ba4-8cac-4f93edc4badc",
"metadata": {},
"source": [
"## Cohorts affected\n",
"Overlapping signals of selection are found in the following cohorts. "
"# SA-1 (*Vgsc*)"
]
},
{
Expand Down Expand Up @@ -117,30 +102,6 @@
"region_signals = region_signals.merge(cohorts)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9222a438-686f-410f-8fd9-02428c2d3095",
"metadata": {
"tags": [
"remove-input"
]
},
"outputs": [],
"source": [
"cohort_links = ['<a href=\"../cohort/' + row['cohort_id'] + '.html\">' + row[\"cohort_label\"] + \"</a>\" for i, row in region_signals.iterrows()]\n",
"html_message = '<li>' + '</li><li>'.join(cohort_links) + '</li>'\n",
"HTML(html_message)"
]
},
{
"cell_type": "markdown",
"id": "b29f7a5a-c33d-4f5a-b6d3-9023ab7ebe55",
"metadata": {},
"source": [
"## Signals and candidate genes"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand Down Expand Up @@ -315,6 +276,45 @@
"plot_region_summary(df=region_signals.reset_index(), region_name=region_name)"
]
},
{
"cell_type": "markdown",
"id": "97da6cd4-0dc2-4ba4-8cac-4f93edc4badc",
"metadata": {},
"source": [
"## Cohorts affected\n",
"Overlapping signals of selection are found in the following cohorts. "
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9222a438-686f-410f-8fd9-02428c2d3095",
"metadata": {
"tags": [
"remove-input"
]
},
"outputs": [],
"source": [
"cohort_links = ['<a href=\"../cohort/' + row['cohort_id'] + '.html\">' + row[\"cohort_label\"] + \"</a>\" for i, row in region_signals.iterrows()]\n",
"html_message = '<li>' + '</li><li>'.join(cohort_links) + '</li>'\n",
"HTML(html_message)"
]
},
{
"cell_type": "markdown",
"id": "b29f7a5a-c33d-4f5a-b6d3-9023ab7ebe55",
"metadata": {},
"source": [
"## Candidate genes\n",
"\n",
"AGAP004707 (*Vgsc*)\n",
"\n",
"Mutations in this gene cause resistance to pyrethroid insecticides and DDT. The most common of these mutations is L995F, which is found across many insect taxa. In *Anopheles gambiae s.l*, we observe many distinct variants under selection, for example, L995F, L995S, and a haplotype containing both V402L and I1527T [(Clarkson *et al.,* 2021)](https://doi.org/10.1111/mec.15845). \n",
"\n",
"This form of resistance was first reported in *Anopheles gambiae* in 1998 [(Martinez-Torres *et al.,* 1998)](https://pubmed.ncbi.nlm.nih.gov/9535162/). Mutants at this locus are now found throughout sub-Saharan Africa. "
]
},
{
"cell_type": "markdown",
"id": "fbf2eacc-ee18-425e-a3ee-ad8e53bda5f9",
Expand Down
83 changes: 44 additions & 39 deletions docs/alert/coeaexf.ipynb → docs/alert/SA-2-Coeaexf.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -31,21 +31,18 @@
},
"outputs": [],
"source": [
"from IPython.display import Markdown, HTML\n",
"from IPython.display import HTML\n",
"import malariagen_data\n",
"import numpy as np\n",
"import pandas as pd\n",
"from pyprojroot import here\n",
"import yaml\n",
"import dask\n",
"dask.config.set(scheduler=dask_scheduler);\n",
"from textwrap import dedent\n",
"\n",
"import geopandas as gpd\n",
"import bokeh.layouts as bklay\n",
"import bokeh.plotting as bkplt\n",
"import bokeh.models as bkmod\n",
"import plotly.express as px\n",
"\n",
"from bokeh.io import output_notebook # enables plot interface in J notebook\n",
"\n",
Expand All @@ -62,23 +59,15 @@
"id": "1f2288aa-fe3d-44c2-88be-aa897d9b4b49",
"metadata": {},
"source": [
"# *Coeaexf*\n",
"\n",
"AGAP006227 (*Coeae1f*) \n",
"AGAP006228 (*Coeae2f*)\n",
"\n",
"Gene amplifications covering these alpha-esterases have been recently associated with resistance to the organophosphate, pirimiphos-methyl [(Nagi *et al.,* 2024)](https://www.biorxiv.org/content/10.1101/2024.02.01.578361v1). Pirimiphos-methyl is widely used in indoor-residual spraying campaigns as the formulation Actellic CS300. \n",
"\n",
"The genes are orthologous to the Est2 and Est3 genes of *Culex pipiens*, which also confer resistance to organophosphates, and were studied intensely in the late 20th century as an example of evolution due to anthropogenic pressures [(Raymond *et al.,* 1998)](https://doi.org/10.1098/rstb.1998.0322). "
"# SA-2 (*Coeaexf*)"
]
},
{
"cell_type": "markdown",
"id": "97da6cd4-0dc2-4ba4-8cac-4f93edc4badc",
"id": "b29f7a5a-c33d-4f5a-b6d3-9023ab7ebe55",
"metadata": {},
"source": [
"## Cohorts affected\n",
"Overlapping signals of selection are found in the following cohorts. "
"## Signals"
]
},
{
Expand Down Expand Up @@ -118,30 +107,6 @@
"region_signals = region_signals.merge(cohorts)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5b39047f-6b12-4402-a973-7dc1cd4f39b1",
"metadata": {
"tags": [
"remove-input"
]
},
"outputs": [],
"source": [
"cohort_links = ['<a href=\"../cohort/' + row['cohort_id'] + '.html\">' + row[\"cohort_label\"] + \"</a>\" for i, row in region_signals.iterrows()]\n",
"html_message = '<li>' + '</li><li>'.join(cohort_links) + '</li>'\n",
"HTML(html_message)"
]
},
{
"cell_type": "markdown",
"id": "b29f7a5a-c33d-4f5a-b6d3-9023ab7ebe55",
"metadata": {},
"source": [
"## Signals and candidate genes"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand Down Expand Up @@ -316,6 +281,46 @@
"plot_region_summary(df=region_signals.reset_index(), region_name=region_name)"
]
},
{
"cell_type": "markdown",
"id": "97da6cd4-0dc2-4ba4-8cac-4f93edc4badc",
"metadata": {},
"source": [
"## Cohorts affected\n",
"Overlapping signals of selection are found in the following cohorts. "
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5b39047f-6b12-4402-a973-7dc1cd4f39b1",
"metadata": {
"tags": [
"remove-input"
]
},
"outputs": [],
"source": [
"cohort_links = ['<a href=\"../cohort/' + row['cohort_id'] + '.html\">' + row[\"cohort_label\"] + \"</a>\" for i, row in region_signals.iterrows()]\n",
"html_message = '<li>' + '</li><li>'.join(cohort_links) + '</li>'\n",
"HTML(html_message)"
]
},
{
"cell_type": "markdown",
"id": "b29c3508",
"metadata": {},
"source": [
"## Candidate genes \n",
"\n",
"AGAP006227 (*Coeae1f*) \n",
"AGAP006228 (*Coeae2f*)\n",
"\n",
"Gene amplifications covering these alpha-esterases have been recently associated with resistance to the organophosphate, pirimiphos-methyl [(Nagi *et al.,* 2024)](https://www.biorxiv.org/content/10.1101/2024.02.01.578361v1). Pirimiphos-methyl is widely used in indoor-residual spraying campaigns as the formulation Actellic CS300. \n",
"\n",
"The genes are orthologous to the Est2 and Est3 genes of *Culex pipiens*, which also confer resistance to organophosphates, and were studied intensely in the late 20th century as an example of evolution due to anthropogenic pressures [(Raymond *et al.,* 1998)](https://doi.org/10.1098/rstb.1998.0322). "
]
},
{
"cell_type": "markdown",
"id": "fbf2eacc-ee18-425e-a3ee-ad8e53bda5f9",
Expand Down
122 changes: 64 additions & 58 deletions workflow/notebooks/selection-alert.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -62,20 +62,41 @@
"id": "1f2288aa-fe3d-44c2-88be-aa897d9b4b49",
"metadata": {},
"source": [
"# example_locus_name\n",
"\n",
"AGAP004707 (*Vgsc*)\n",
"\n",
"Mutations in this gene cause resistance to pyrethroid insecticides and DDT."
"# SA-1"
]
},
{
"cell_type": "markdown",
"id": "97da6cd4-0dc2-4ba4-8cac-4f93edc4badc",
"id": "b29f7a5a-c33d-4f5a-b6d3-9023ab7ebe55",
"metadata": {},
"source": [
"## Cohorts affected\n",
"Overlapping signals of selection are found in the following cohorts. "
"## Signals"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9a2a86dd-58c7-4037-b99c-53ede4c54f87",
"metadata": {
"tags": [
"remove-input",
"remove-output"
]
},
"outputs": [],
"source": [
"extra_params = dict()\n",
"if use_gcs_cache:\n",
" extra_params[\"url\"] = \"simplecache::gs://vo_agam_release\"\n",
" extra_params[\"simplecache\"] = dict(cache_storage=(here() / \"gcs_cache\").as_posix())\n",
"\n",
"ag3 = malariagen_data.Ag3(\n",
" # pin the version of the cohorts analysis for reproducibility\n",
" cohorts_analysis=cohorts_analysis,\n",
" results_cache=(here() / \"malariagen_data_cache\").as_posix(),\n",
" **extra_params,\n",
")\n",
"ag3"
]
},
{
Expand Down Expand Up @@ -115,56 +136,6 @@
"region_signals = region_signals.merge(cohorts)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "346bbbd3-c0f8-4f44-a3ce-e417080d2245",
"metadata": {
"tags": [
"remove-input"
]
},
"outputs": [],
"source": [
"cohort_links = ['<a href=\"../cohort/' + row['cohort_id'] + '.html\">' + row[\"cohort_label\"] + \"</a>\" for i, row in region_signals.iterrows()]\n",
"html_message = '<li>' + '</li><li>'.join(cohort_links) + '</li>'\n",
"HTML(html_message)"
]
},
{
"cell_type": "markdown",
"id": "b29f7a5a-c33d-4f5a-b6d3-9023ab7ebe55",
"metadata": {},
"source": [
"## Signals and candidate genes"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9a2a86dd-58c7-4037-b99c-53ede4c54f87",
"metadata": {
"tags": [
"remove-input",
"remove-output"
]
},
"outputs": [],
"source": [
"extra_params = dict()\n",
"if use_gcs_cache:\n",
" extra_params[\"url\"] = \"simplecache::gs://vo_agam_release\"\n",
" extra_params[\"simplecache\"] = dict(cache_storage=(here() / \"gcs_cache\").as_posix())\n",
"\n",
"ag3 = malariagen_data.Ag3(\n",
" # pin the version of the cohorts analysis for reproducibility\n",
" cohorts_analysis=cohorts_analysis,\n",
" results_cache=(here() / \"malariagen_data_cache\").as_posix(),\n",
" **extra_params,\n",
")\n",
"ag3"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand Down Expand Up @@ -313,6 +284,41 @@
"plot_region_summary(df=region_signals.reset_index(), region_name=region_name)"
]
},
{
"cell_type": "markdown",
"id": "97da6cd4-0dc2-4ba4-8cac-4f93edc4badc",
"metadata": {},
"source": [
"## Cohorts affected\n",
"Overlapping signals of selection are found in the following cohorts. "
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "346bbbd3-c0f8-4f44-a3ce-e417080d2245",
"metadata": {
"tags": [
"remove-input"
]
},
"outputs": [],
"source": [
"cohort_links = ['<a href=\"../cohort/' + row['cohort_id'] + '.html\">' + row[\"cohort_label\"] + \"</a>\" for i, row in region_signals.iterrows()]\n",
"html_message = '<li>' + '</li><li>'.join(cohort_links) + '</li>'\n",
"HTML(html_message)"
]
},
{
"cell_type": "markdown",
"id": "db71a1cd",
"metadata": {},
"source": [
"## Candidate genes\n",
"\n",
"AGAP004707 (*Vgsc*) - The Voltage-gated sodium channel (VGSC) is the target of pyrethroids and DDT. Mutations in this gene are associated with knockdown resistance (kdr) to pyrethroids and DDT..."
]
},
{
"cell_type": "markdown",
"id": "fbf2eacc-ee18-425e-a3ee-ad8e53bda5f9",
Expand Down

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