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Fixed all histograms and created new 2024EBP histo
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@ccaio
ccaio committed Jan 15, 2024
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19 changes: 13 additions & 6 deletions static/projects/ebp.md
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Expand Up @@ -43,24 +43,31 @@ Click on report to see and download individually.

### Contribution of EBP to Whole Genome Sequencing of Eukaryotic Taxa

**Progress of EBP in 2023**
**Progress of EBP in 2024**
:::grid{container direction="row" spacing="1" item xs=12}

::report{report="histogram" x="min(assembly_date)>2023 AND bioproject=PRJNA533106" rank="species" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2023-01,2024,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic species generated by EBP affiliates each month in 2023" item xs=6}
::report{report="histogram" x="min(assembly_date)>2024 AND bioproject=PRJNA533106" rank="species" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2024-01,2025,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic species generated by EBP affiliates each month in 2024" item xs=6}

::report{report="histogram" x="min(assembly_date)>2023 AND bioproject=PRJNA533106" rank="family" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" includeEstimates=true excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2023-01,2024,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic families generated by EBP affiliates each month in 2023" item xs=6}
::report{report="histogram" x="min(assembly_date)>2024 AND bioproject=PRJNA533106" rank="family" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" includeEstimates=true excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2024-01,2025,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic families generated by EBP affiliates each month in 2024" item xs=6}

:::
Click on report to see and download individually.

:::grid{container direction="row" spacing="1" class="padded"}
:::

:::grid{container direction="row" toggle title="Progress of EBP in 2023" spacing="1"}

::report{report="histogram" x="min(assembly_date)>2023 AND bioproject=PRJNA533106" rank="species" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2023-01,2024,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic species generated by EBP affiliates each month in 2023" item xs=6}

::report{report="histogram" x="min(assembly_date)>2023 AND bioproject=PRJNA533106" rank="family" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" includeEstimates=true excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2023-01,2024,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic families generated by EBP affiliates each month in 2023" item xs=6}
:::

:::grid{container direction="row" toggle title="Progress of EBP in 2022" spacing="1"}

::report{report="histogram" x="max(assembly_date)>2022 AND bioproject=PRJNA533106" rank="species" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2022-01,2023,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic species generated by EBP affiliates each month in 2022" item xs=6}
::report{report="histogram" x="min(assembly_date)>2022 AND bioproject=PRJNA533106" rank="species" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2022-01,2023,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic species generated by EBP affiliates each month in 2022" item xs=6}

::report{report="histogram" x="max(assembly_date)>2022 AND bioproject=PRJNA533106" rank="family" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" includeEstimates=true excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2022-01,2023,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic families generated by EBP affiliates each month in 2022" item xs=6}
::report{report="histogram" x="min(assembly_date)>2022 AND bioproject=PRJNA533106" rank="family" result="taxon" cat="assembly_level=contig,scaffold,chromosome,complete genome" includeEstimates=true excludeAncestral="bioproject" excludeMissing="bioproject" stacked="true" xOpts="2022-01,2023,,,Assembly date (month)" yOpts="0,1000,1" caption="Number of assemblies for eukaryotic families generated by EBP affiliates each month in 2022" item xs=6}
:::

:::grid{container direction="row" spacing="1" class="padded"}
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:::grid{container direction="row" spacing="1" item xs=12}

::report{report="histogram" x="tax_tree(2759) AND long_list AND bioproject=PRJNA533106 AND insdc_open=EBP" rank="species" includeEstimates="false" cat="kingdom" stacked="true" xOpts=",,55,,EBP Affiliate" caption="Assemblies available on INSDC for target species across EBP-affiliated projects. Note that umbrella projects will inherit counts from their sub-projects and that overlapping targets sequenced by at least one EBP affiliate will appear as complete in all projects targeting that taxon" item xs=6}
::report{report="histogram" x="tax_tree(2759) AND long_list AND bioproject=PRJNA533106" rank="species" includeEstimates="false" cat="kingdom" stacked="true" xOpts=",,55,,EBP Affiliate" caption="Assemblies available on INSDC for target species across EBP-affiliated projects. Note that umbrella projects will inherit counts from their sub-projects and that overlapping targets sequenced by at least one EBP affiliate will appear as complete in all projects targeting that taxon" item xs=6}

::report{report="histogram" x="tax_tree(2759) AND long_list AND sequencing_status=in_progress" rank="species" includeEstimates="false" cat="kingdom" stacked="true" xOpts=",,55,,EBP Affiliate" caption="Number of target species across EBP affiliated projects with genome sequencing in progress. Note that species in multiple lists will be counted as in progress for all projects if sequencing has been initiated by at least one of the projects" item xs=6}

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7 changes: 4 additions & 3 deletions static/projects/reports/progress_histo.md
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```report
report: histogram
x: "long_list={{project}} AND sequencing_status_{{lc_project}}"
y: "sequencing_status_{{lc_project}}"
x: "sequencing_status_{{lc_project}} AND long_list={{project}}"
xField: "sequencing_status_{{lc_project}}"
rank: species
cat: "sequencing_status_{{lc_project}}=sample_collected,sample_acquired,in_progress,data_generation,in_assembly,open,insdc_open,published"
includeEstimates: true
excludeAncestral: sequencing_status_{{lc_project}}
excludeMissing: sequencing_status_{{lc_project}}
xOpts: ",,1,,Sequencing Status"
xOpts: ";;;;Sequencing Status"
stacked: True
caption: "Current status of {{project}} target species"
item: true
xs: 6
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