diff --git a/.gitignore b/.gitignore index b7de5c46..f884e0ab 100644 --- a/.gitignore +++ b/.gitignore @@ -65,9 +65,6 @@ instance/ # Scrapy stuff: .scrapy -# Sphinx documentation -docs/_build/ - # PyBuilder target/ @@ -135,10 +132,10 @@ notebooks/zika_tree.json source/docs/_build .vscode/ -docs/cartography.aux -docs/cartography.bbl -docs/cartography.blg -docs/cartography.suppinfo +manuscript/cartography.aux +manuscript/cartography.bbl +manuscript/cartography.blg +manuscript/cartography.suppinfo # Adding gridsearch but not results **/seasonal-flu-nextstrain/results/* diff --git a/Snakefile b/Snakefile index d423dacc..74096391 100644 --- a/Snakefile +++ b/Snakefile @@ -65,9 +65,9 @@ wildcard_constraints: rule all: input: # Static version of the paper. - "docs/cartography.pdf", + "manuscript/cartography.pdf", # Interactive version of the paper. - "docs/cartography.html", + #"manuscript/cartography.html", # Include rules for each pathogen. include: "simulations/Snakefile" @@ -86,4 +86,4 @@ rule pathogens: *rules.sarscov2_test.input, # Include rules for the manuscript. -include: "docs/Snakefile" +include: "manuscript/Snakefile" diff --git a/docs/Snakefile b/manuscript/Snakefile similarity index 73% rename from docs/Snakefile rename to manuscript/Snakefile index d14f6296..4e2f786d 100644 --- a/docs/Snakefile +++ b/manuscript/Snakefile @@ -1,6 +1,6 @@ rule manuscript: input: - "docs/cartography.pdf", + "manuscript/cartography.pdf", rule within_between_stats: input: @@ -9,8 +9,8 @@ rule within_between_stats: within_between_df_sars_training = "sars-cov-2-nextstrain/results/full_within_between_stats.csv", within_between_df_sars_test = "sars-cov-2-nextstrain-2022-2023/results/full_within_between_stats.csv", output: - flu_png = "docs/figures/within_between_influenza.png", - sars_png = "docs/figures/within_between_sars.png", + flu_png = "manuscript/figures/within_between_influenza.png", + sars_png = "manuscript/figures/within_between_sars.png", conda: "../cartography.yml" notebook: "../notebooks/2023-07-24WithinVBetweenFigure.ipynb" @@ -27,7 +27,7 @@ rule concat_mutation_tables: "sars-cov-2-nextstrain-2022-2023/results/mutation_table_for_Nextclade_pango.csv", ] output: - csv_table = "docs/tables/mutation_table.csv", + csv_table = "manuscript/tables/mutation_table.csv", conda: "../cartography.yml" shell: """ @@ -45,8 +45,8 @@ rule concat_HDBSCAN_tables: "sars-cov-2-nextstrain/results/optimal_cluster_accuracy_and_parameters_for_Nextclade_pango_collapsed.csv", ] output: - fullKDE = "docs/tables/total_HDBSCAN_table.csv", - table = "docs/tables/accuracy_table.tex", + fullKDE = "manuscript/tables/total_HDBSCAN_table.csv", + table = "manuscript/tables/accuracy_table.tex", params: disease_names = ["Influenza H3N2", "SARS-CoV-2 (Nextstrain clade)", "SARS-CoV-2 (Nextclade pango)"], conda: "../cartography.yml" @@ -69,7 +69,7 @@ rule concat_within_between_figure_table: "sars-cov-2-nextstrain-2022-2023/results/full_within_between_stats.csv", ] output: - csv_table = "docs/tables/total_within_between_stats.csv", + csv_table = "manuscript/tables/total_within_between_stats.csv", conda: "../cartography.yml" shell: """ @@ -89,7 +89,7 @@ rule concat_accessions_and_authors_tables: "sars-cov-2-nextstrain-2022-2023/results/accessions_and_authors.tsv", ], output: - authors="docs/tables/accessions_and_authors.tsv", + authors="manuscript/tables/accessions_and_authors.tsv", conda: "../cartography.yml" shell: """ @@ -99,22 +99,22 @@ rule concat_accessions_and_authors_tables: rule manuscript_pdf: input: *rules.pathogens.input, - "docs/figures/simulated-influenza-like-with-no-reassortment-scores-by-parameters.png", - "docs/figures/simulated-coronavirus-like-with-moderate-recombination-rate-scores-by-parameters.png", - "docs/figures/simulated-populations-representative-embeddings.png", - "docs/figures/simulated-populations-representative-mds-embeddings.png", - "docs/figures/flu-2018-2020-replication-of-cluster-accuracy.png", - "docs/figures/sarscov2-test-replication-of-cluster-accuracy.png", - manuscript="docs/cartography.tex", - bibliography="docs/cartography.bib", - accuracy_table="docs/tables/accuracy_table.tex", - mutation_table="docs/tables/mutation_table.csv", - within_between_stats_table="docs/tables/total_within_between_stats.csv", - within_between_influenza_figure="docs/figures/within_between_influenza.png", - within_between_sars_figure="docs/figures/within_between_sars.png", - accessions_and_authors_table="docs/tables/accessions_and_authors.tsv", + "manuscript/figures/simulated-influenza-like-with-no-reassortment-scores-by-parameters.png", + "manuscript/figures/simulated-coronavirus-like-with-moderate-recombination-rate-scores-by-parameters.png", + "manuscript/figures/simulated-populations-representative-embeddings.png", + "manuscript/figures/simulated-populations-representative-mds-embeddings.png", + "manuscript/figures/flu-2018-2020-replication-of-cluster-accuracy.png", + "manuscript/figures/sarscov2-test-replication-of-cluster-accuracy.png", + manuscript="manuscript/cartography.tex", + bibliography="manuscript/cartography.bib", + accuracy_table="manuscript/tables/accuracy_table.tex", + mutation_table="manuscript/tables/mutation_table.csv", + within_between_stats_table="manuscript/tables/total_within_between_stats.csv", + within_between_influenza_figure="manuscript/figures/within_between_influenza.png", + within_between_sars_figure="manuscript/figures/within_between_sars.png", + accessions_and_authors_table="manuscript/tables/accessions_and_authors.tsv", output: - manuscript = "docs/cartography.pdf", + manuscript = "manuscript/cartography.pdf", conda: "../cartography.yml" shell: """ @@ -129,7 +129,7 @@ rule manuscript_html: template = "pandoc-scholar.html", css = "pandoc-scholar.css" output: - manuscript = "cartography.html" + manuscript = "manuscript/cartography.html" conda: "../cartography.yml" shell: """ diff --git a/docs/build.sh 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b/manuscript/figures/sarscov2-test-embeddings-by-cluster-vs-Nextstrain_clade.png similarity index 100% rename from docs/figures/sarscov2-test-embeddings-by-cluster-vs-Nextstrain_clade.png rename to manuscript/figures/sarscov2-test-embeddings-by-cluster-vs-Nextstrain_clade.png diff --git a/docs/figures/sarscov2-test-euclidean-distance-by-genetic-distance.png b/manuscript/figures/sarscov2-test-euclidean-distance-by-genetic-distance.png similarity index 100% rename from docs/figures/sarscov2-test-euclidean-distance-by-genetic-distance.png rename to manuscript/figures/sarscov2-test-euclidean-distance-by-genetic-distance.png diff --git a/docs/figures/sarscov2-test-mds-by-Nextclade_pango_collapsed-clade.html b/manuscript/figures/sarscov2-test-mds-by-Nextclade_pango_collapsed-clade.html similarity index 100% rename from docs/figures/sarscov2-test-mds-by-Nextclade_pango_collapsed-clade.html rename to manuscript/figures/sarscov2-test-mds-by-Nextclade_pango_collapsed-clade.html diff --git a/docs/figures/sarscov2-test-mds-by-Nextclade_pango_collapsed-clade.png b/manuscript/figures/sarscov2-test-mds-by-Nextclade_pango_collapsed-clade.png similarity index 100% rename from docs/figures/sarscov2-test-mds-by-Nextclade_pango_collapsed-clade.png rename to manuscript/figures/sarscov2-test-mds-by-Nextclade_pango_collapsed-clade.png diff --git a/docs/figures/sarscov2-test-mds-by-Nextstrain_clade-clade.html b/manuscript/figures/sarscov2-test-mds-by-Nextstrain_clade-clade.html similarity index 100% rename from docs/figures/sarscov2-test-mds-by-Nextstrain_clade-clade.html rename to manuscript/figures/sarscov2-test-mds-by-Nextstrain_clade-clade.html diff --git a/docs/figures/sarscov2-test-mds-by-Nextstrain_clade-clade.png b/manuscript/figures/sarscov2-test-mds-by-Nextstrain_clade-clade.png similarity index 100% rename from docs/figures/sarscov2-test-mds-by-Nextstrain_clade-clade.png rename to manuscript/figures/sarscov2-test-mds-by-Nextstrain_clade-clade.png diff --git a/docs/figures/sarscov2-test-pca-by-Nextclade_pango_collapsed-clade.html b/manuscript/figures/sarscov2-test-pca-by-Nextclade_pango_collapsed-clade.html similarity index 100% rename from docs/figures/sarscov2-test-pca-by-Nextclade_pango_collapsed-clade.html rename to manuscript/figures/sarscov2-test-pca-by-Nextclade_pango_collapsed-clade.html diff --git a/docs/figures/sarscov2-test-pca-by-Nextclade_pango_collapsed-clade.png b/manuscript/figures/sarscov2-test-pca-by-Nextclade_pango_collapsed-clade.png similarity index 100% rename from docs/figures/sarscov2-test-pca-by-Nextclade_pango_collapsed-clade.png rename to manuscript/figures/sarscov2-test-pca-by-Nextclade_pango_collapsed-clade.png diff --git a/docs/figures/sarscov2-test-pca-by-Nextstrain_clade-clade.html b/manuscript/figures/sarscov2-test-pca-by-Nextstrain_clade-clade.html similarity index 100% rename from docs/figures/sarscov2-test-pca-by-Nextstrain_clade-clade.html rename to manuscript/figures/sarscov2-test-pca-by-Nextstrain_clade-clade.html diff --git a/docs/figures/sarscov2-test-pca-by-Nextstrain_clade-clade.png b/manuscript/figures/sarscov2-test-pca-by-Nextstrain_clade-clade.png similarity index 100% rename from docs/figures/sarscov2-test-pca-by-Nextstrain_clade-clade.png rename to manuscript/figures/sarscov2-test-pca-by-Nextstrain_clade-clade.png diff --git a/docs/figures/sarscov2-test-pca-explained-variance-for-Nextclade_pango_collapsed.png b/manuscript/figures/sarscov2-test-pca-explained-variance-for-Nextclade_pango_collapsed.png similarity index 100% rename from docs/figures/sarscov2-test-pca-explained-variance-for-Nextclade_pango_collapsed.png rename to manuscript/figures/sarscov2-test-pca-explained-variance-for-Nextclade_pango_collapsed.png diff --git a/docs/figures/sarscov2-test-pca-explained-variance-for-Nextstrain_clade.png b/manuscript/figures/sarscov2-test-pca-explained-variance-for-Nextstrain_clade.png similarity index 100% rename from docs/figures/sarscov2-test-pca-explained-variance-for-Nextstrain_clade.png rename to manuscript/figures/sarscov2-test-pca-explained-variance-for-Nextstrain_clade.png diff --git a/docs/figures/sarscov2-test-replication-of-cluster-accuracy.png b/manuscript/figures/sarscov2-test-replication-of-cluster-accuracy.png similarity index 100% rename from docs/figures/sarscov2-test-replication-of-cluster-accuracy.png rename to manuscript/figures/sarscov2-test-replication-of-cluster-accuracy.png diff --git a/docs/figures/simulated-coronavirus-like-with-moderate-recombination-rate-scores-by-parameters.png b/manuscript/figures/simulated-coronavirus-like-with-moderate-recombination-rate-scores-by-parameters.png similarity index 100% rename from docs/figures/simulated-coronavirus-like-with-moderate-recombination-rate-scores-by-parameters.png rename to manuscript/figures/simulated-coronavirus-like-with-moderate-recombination-rate-scores-by-parameters.png diff --git a/docs/figures/simulated-influenza-like-with-no-reassortment-scores-by-parameters.png b/manuscript/figures/simulated-influenza-like-with-no-reassortment-scores-by-parameters.png similarity index 100% rename from docs/figures/simulated-influenza-like-with-no-reassortment-scores-by-parameters.png rename to manuscript/figures/simulated-influenza-like-with-no-reassortment-scores-by-parameters.png diff --git a/docs/figures/simulated-populations-representative-embeddings.png b/manuscript/figures/simulated-populations-representative-embeddings.png similarity index 100% rename from docs/figures/simulated-populations-representative-embeddings.png rename to manuscript/figures/simulated-populations-representative-embeddings.png diff --git a/docs/figures/simulated-populations-representative-mds-embeddings.png b/manuscript/figures/simulated-populations-representative-mds-embeddings.png similarity index 100% rename from docs/figures/simulated-populations-representative-mds-embeddings.png rename to manuscript/figures/simulated-populations-representative-mds-embeddings.png diff --git a/docs/figures/within_between_influenza.png b/manuscript/figures/within_between_influenza.png similarity index 100% rename from docs/figures/within_between_influenza.png rename to manuscript/figures/within_between_influenza.png diff --git a/docs/figures/within_between_sars.png b/manuscript/figures/within_between_sars.png similarity index 100% rename from docs/figures/within_between_sars.png rename to manuscript/figures/within_between_sars.png diff --git a/docs/plos2015.bst b/manuscript/plos2015.bst similarity index 100% rename from docs/plos2015.bst rename to manuscript/plos2015.bst diff --git a/docs/tables/accessions_and_authors.tsv b/manuscript/tables/accessions_and_authors.tsv similarity index 100% rename from docs/tables/accessions_and_authors.tsv rename to manuscript/tables/accessions_and_authors.tsv diff --git a/docs/tables/accuracy_table.tex b/manuscript/tables/accuracy_table.tex similarity index 100% rename from docs/tables/accuracy_table.tex rename to manuscript/tables/accuracy_table.tex diff --git a/docs/tables/mutation_table.csv b/manuscript/tables/mutation_table.csv similarity index 100% rename from docs/tables/mutation_table.csv rename to manuscript/tables/mutation_table.csv diff --git a/docs/tables/sars-cov-2-recombinant-distances.tex b/manuscript/tables/sars-cov-2-recombinant-distances.tex similarity index 100% rename from docs/tables/sars-cov-2-recombinant-distances.tex rename to manuscript/tables/sars-cov-2-recombinant-distances.tex diff --git a/docs/tables/total_within_between_stats.csv b/manuscript/tables/total_within_between_stats.csv similarity index 100% rename from docs/tables/total_within_between_stats.csv rename to manuscript/tables/total_within_between_stats.csv diff --git a/sars-cov-2-nextstrain-2022-2023/Snakefile b/sars-cov-2-nextstrain-2022-2023/Snakefile index b5774f54..dcb2e57b 100644 --- a/sars-cov-2-nextstrain-2022-2023/Snakefile +++ b/sars-cov-2-nextstrain-2022-2023/Snakefile @@ -1,15 +1,15 @@ rule sarscov2_test: input: - expand("docs/figures/sarscov2-test-embeddings-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-test-embeddings-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-test-embeddings-by-cluster-vs-{clade_membership}.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-test-embeddings-by-cluster-vs-{clade_membership}.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-test-pca-explained-variance-for-{clade_membership}.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-test-pca-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-test-pca-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-test-mds-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-test-mds-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - "docs/figures/sarscov2-test-euclidean-distance-by-genetic-distance.png", + expand("manuscript/figures/sarscov2-test-embeddings-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-test-embeddings-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-test-embeddings-by-cluster-vs-{clade_membership}.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-test-embeddings-by-cluster-vs-{clade_membership}.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-test-pca-explained-variance-for-{clade_membership}.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-test-pca-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-test-pca-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-test-mds-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-test-mds-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + "manuscript/figures/sarscov2-test-euclidean-distance-by-genetic-distance.png", "auspice/cartography_ncov_2022-2023.json", "sars-cov-2-nextstrain-2022-2023/results/recombinant_distances.csv", expand("sars-cov-2-nextstrain-2022-2023/results/mutation_table_for_{clade_membership}.csv", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), @@ -592,7 +592,7 @@ rule sarscov2_test_create_scatterplot_figure: scatterplot_tsne = "sars-cov-2-nextstrain-2022-2023/results/scatterplot_t-sne.csv", scatterplot_umap = "sars-cov-2-nextstrain-2022-2023/results/scatterplot_umap.csv", output: - scatterplot = "docs/figures/sarscov2-test-euclidean-distance-by-genetic-distance.png", + scatterplot = "manuscript/figures/sarscov2-test-euclidean-distance-by-genetic-distance.png", conda: "../cartography.yml" notebook: "../notebooks/2022-09-26-scatterplot-figure.py.ipynb" @@ -670,7 +670,7 @@ rule sarscov2_test_concat_recombinant_distances: distances=expand("sars-cov-2-nextstrain-2022-2023/results/recombinant_distances_for_{method}.csv", method=EMBEDDING_METHODS), output: distances="sars-cov-2-nextstrain-2022-2023/results/recombinant_distances.csv", - distances_latex="docs/tables/sars-cov-2-recombinant-distances.tex", + distances_latex="manuscript/tables/sars-cov-2-recombinant-distances.tex", conda: "../cartography.yml" params: latex_precision=2, @@ -766,15 +766,15 @@ rule sarscov2_test_create_notebook_docs: accuracy_table="sars-cov-2-nextstrain-2022-2023/results/full_HDBSCAN_metadata_for_{clade_membership}.csv", explained_variance_pca = "sars-cov-2-nextstrain-2022-2023/results/explained_variance_pca.csv", output: - fullChart="docs/figures/sarscov2-test-embeddings-by-{clade_membership}-clade.html", - fullChartPNG="docs/figures/sarscov2-test-embeddings-by-{clade_membership}-clade.png", - fullChartHDBSCAN="docs/figures/sarscov2-test-embeddings-by-cluster-vs-{clade_membership}.html", - fullChartHDBSCANPNG="docs/figures/sarscov2-test-embeddings-by-cluster-vs-{clade_membership}.png", - Explained_variance_PCA="docs/figures/sarscov2-test-pca-explained-variance-for-{clade_membership}.png", - PCA_Supplement="docs/figures/sarscov2-test-pca-by-{clade_membership}-clade.html", - PCA_Supplement_PNG="docs/figures/sarscov2-test-pca-by-{clade_membership}-clade.png", - MDS_Supplement="docs/figures/sarscov2-test-mds-by-{clade_membership}-clade.html", - MDS_Supplement_PNG="docs/figures/sarscov2-test-mds-by-{clade_membership}-clade.png", + fullChart="manuscript/figures/sarscov2-test-embeddings-by-{clade_membership}-clade.html", + fullChartPNG="manuscript/figures/sarscov2-test-embeddings-by-{clade_membership}-clade.png", + fullChartHDBSCAN="manuscript/figures/sarscov2-test-embeddings-by-cluster-vs-{clade_membership}.html", + fullChartHDBSCANPNG="manuscript/figures/sarscov2-test-embeddings-by-cluster-vs-{clade_membership}.png", + Explained_variance_PCA="manuscript/figures/sarscov2-test-pca-explained-variance-for-{clade_membership}.png", + PCA_Supplement="manuscript/figures/sarscov2-test-pca-by-{clade_membership}-clade.html", + PCA_Supplement_PNG="manuscript/figures/sarscov2-test-pca-by-{clade_membership}-clade.png", + MDS_Supplement="manuscript/figures/sarscov2-test-mds-by-{clade_membership}-clade.html", + MDS_Supplement_PNG="manuscript/figures/sarscov2-test-mds-by-{clade_membership}-clade.png", params: clade_membership=lambda wildcards: wildcards.clade_membership, pca_label=lambda wildcards: f"pca_label_for_{wildcards.clade_membership}", @@ -1005,7 +1005,7 @@ rule sarscov2_test_replication_plot_cluster_accuracy: input: accuracies="sars-cov-2-nextstrain-2022-2023/results/replication_analysis_cluster_accuracy.csv", output: - accuracies="docs/figures/sarscov2-test-replication-of-cluster-accuracy.png", + accuracies="manuscript/figures/sarscov2-test-replication-of-cluster-accuracy.png", conda: "../cartography.yml" notebook: "../notebooks/plot-replication-of-cluster-accuracy.py.ipynb" diff --git a/sars-cov-2-nextstrain/Snakefile b/sars-cov-2-nextstrain/Snakefile index af4d0eff..2355b873 100644 --- a/sars-cov-2-nextstrain/Snakefile +++ b/sars-cov-2-nextstrain/Snakefile @@ -5,15 +5,15 @@ SARS_COV_2_CLADE_MEMBERSHIPS = [ rule sarscov2: input: - expand("docs/figures/sarscov2-embeddings-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-embeddings-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-embeddings-by-cluster-vs-{clade_membership}.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-embeddings-by-cluster-vs-{clade_membership}.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-pca-explained-variance-for-{clade_membership}.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-pca-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - expand("docs/figures/sarscov2-pca-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), - "docs/figures/sarscov2-euclidean-distance-by-genetic-distance.png", - "docs/figures/sarscov2-pc1-vs-bases-missing.png", + expand("manuscript/figures/sarscov2-embeddings-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-embeddings-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-embeddings-by-cluster-vs-{clade_membership}.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-embeddings-by-cluster-vs-{clade_membership}.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-pca-explained-variance-for-{clade_membership}.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-pca-by-{clade_membership}-clade.html", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + expand("manuscript/figures/sarscov2-pca-by-{clade_membership}-clade.png", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), + "manuscript/figures/sarscov2-euclidean-distance-by-genetic-distance.png", + "manuscript/figures/sarscov2-pc1-vs-bases-missing.png", "auspice/cartography_ncov_2020-2022.json", expand("sars-cov-2-nextstrain/results/mutation_table_for_{clade_membership}.csv", clade_membership=SARS_COV_2_CLADE_MEMBERSHIPS), @@ -156,7 +156,7 @@ rule sarscov2_bases_missing_vs_pc1: metadata = "sars-cov-2-nextstrain/data/metadata.tsv", pca = "sars-cov-2-nextstrain/results/embed_pca_before.csv", output: - figure = "docs/figures/sarscov2-pc1-vs-bases-missing.png" + figure = "manuscript/figures/sarscov2-pc1-vs-bases-missing.png" params: bootstrap = 100, conda: "../cartography.yml" @@ -631,7 +631,7 @@ rule sarscov2_create_scatterplot_figure: scatterplot_tsne = "sars-cov-2-nextstrain/results/scatterplot_t-sne.csv", scatterplot_umap = "sars-cov-2-nextstrain/results/scatterplot_umap.csv", output: - scatterplot = "docs/figures/sarscov2-euclidean-distance-by-genetic-distance.png", + scatterplot = "manuscript/figures/sarscov2-euclidean-distance-by-genetic-distance.png", conda: "../cartography.yml" notebook: "../notebooks/2022-09-26-scatterplot-figure.py.ipynb" @@ -763,15 +763,15 @@ rule sarscov2_create_notebook_docs: accuracy_table="sars-cov-2-nextstrain/results/optimal_cluster_accuracy_and_parameters_for_{clade_membership}.csv", explained_variance_pca = "sars-cov-2-nextstrain/results/explained_variance_pca.csv", output: - fullChart="docs/figures/sarscov2-embeddings-by-{clade_membership}-clade.html", - fullChartPNG="docs/figures/sarscov2-embeddings-by-{clade_membership}-clade.png", - fullChartHDBSCAN="docs/figures/sarscov2-embeddings-by-cluster-vs-{clade_membership}.html", - fullChartHDBSCANPNG="docs/figures/sarscov2-embeddings-by-cluster-vs-{clade_membership}.png", - Explained_variance_PCA="docs/figures/sarscov2-pca-explained-variance-for-{clade_membership}.png", - PCA_Supplement="docs/figures/sarscov2-pca-by-{clade_membership}-clade.html", - PCA_Supplement_PNG="docs/figures/sarscov2-pca-by-{clade_membership}-clade.png", - MDS_Supplement="docs/figures/sarscov2-mds-by-{clade_membership}-clade.html", - MDS_Supplement_PNG="docs/figures/sarscov2-mds-by-{clade_membership}-clade.png", + fullChart="manuscript/figures/sarscov2-embeddings-by-{clade_membership}-clade.html", + fullChartPNG="manuscript/figures/sarscov2-embeddings-by-{clade_membership}-clade.png", + fullChartHDBSCAN="manuscript/figures/sarscov2-embeddings-by-cluster-vs-{clade_membership}.html", + fullChartHDBSCANPNG="manuscript/figures/sarscov2-embeddings-by-cluster-vs-{clade_membership}.png", + Explained_variance_PCA="manuscript/figures/sarscov2-pca-explained-variance-for-{clade_membership}.png", + PCA_Supplement="manuscript/figures/sarscov2-pca-by-{clade_membership}-clade.html", + PCA_Supplement_PNG="manuscript/figures/sarscov2-pca-by-{clade_membership}-clade.png", + MDS_Supplement="manuscript/figures/sarscov2-mds-by-{clade_membership}-clade.html", + MDS_Supplement_PNG="manuscript/figures/sarscov2-mds-by-{clade_membership}-clade.png", params: clade_membership=lambda wildcards: wildcards.clade_membership, pca_label=lambda wildcards: f"pca_label_for_{wildcards.clade_membership}", diff --git a/seasonal-flu-nextstrain-2018-2020/Snakefile b/seasonal-flu-nextstrain-2018-2020/Snakefile index bccc4e51..e385f7b6 100644 --- a/seasonal-flu-nextstrain-2018-2020/Snakefile +++ b/seasonal-flu-nextstrain-2018-2020/Snakefile @@ -1,11 +1,11 @@ rule seasonal_flu_test: input: - "docs/figures/flu-2018-2020-ha-embeddings-by-clade.png", - "docs/figures/flu-2018-2020-ha-embeddings-by-clade.html", - "docs/figures/flu-2018-2020-ha-embeddings-by-cluster.html", - "docs/figures/flu-2018-2020-ha-embeddings-by-cluster.png", - "docs/figures/flu-2018-2020-mds-by-clade.html", - "docs/figures/flu-2018-2020-mds-by-clade.png", + "manuscript/figures/flu-2018-2020-ha-embeddings-by-clade.png", + "manuscript/figures/flu-2018-2020-ha-embeddings-by-clade.html", + "manuscript/figures/flu-2018-2020-ha-embeddings-by-cluster.html", + "manuscript/figures/flu-2018-2020-ha-embeddings-by-cluster.png", + "manuscript/figures/flu-2018-2020-mds-by-clade.html", + "manuscript/figures/flu-2018-2020-mds-by-clade.png", "auspice/cartography_flu-seasonal-h3n2-ha-2018-2020.json", "seasonal-flu-nextstrain-2018-2020/results/mutation_table.csv", "seasonal-flu-nextstrain-2018-2020/results/full_within_between_stats.csv" @@ -574,12 +574,12 @@ rule seasonal_flu_test_create_notebook_docs: accuracy_table="seasonal-flu-nextstrain-2018-2020/results/full_HDBSCAN_metadata.csv", explained_variance_pca = "seasonal-flu-nextstrain-2018-2020/results/explained_variance_pca_sequences.csv", output: - fullChartPNG = "docs/figures/flu-2018-2020-ha-embeddings-by-clade.png", - fullChart = "docs/figures/flu-2018-2020-ha-embeddings-by-clade.html", - fullChartHDBSCAN20182020="docs/figures/flu-2018-2020-ha-embeddings-by-cluster.html", - fullChartHDBSCANPNG20182020="docs/figures/flu-2018-2020-ha-embeddings-by-cluster.png", - MDS_Supplement = "docs/figures/flu-2018-2020-mds-by-clade.html", - MDS_Supplement_PNG = "docs/figures/flu-2018-2020-mds-by-clade.png", + fullChartPNG = "manuscript/figures/flu-2018-2020-ha-embeddings-by-clade.png", + fullChart = "manuscript/figures/flu-2018-2020-ha-embeddings-by-clade.html", + fullChartHDBSCAN20182020="manuscript/figures/flu-2018-2020-ha-embeddings-by-cluster.html", + fullChartHDBSCANPNG20182020="manuscript/figures/flu-2018-2020-ha-embeddings-by-cluster.png", + MDS_Supplement = "manuscript/figures/flu-2018-2020-mds-by-clade.html", + MDS_Supplement_PNG = "manuscript/figures/flu-2018-2020-mds-by-clade.png", conda: "../cartography.yml" notebook: "2021-03-09Notebook.ipynb" @@ -917,7 +917,7 @@ rule seasonal_flu_test_replication_plot_cluster_accuracy: input: accuracies="seasonal-flu-nextstrain-2018-2020/results/replication_analysis_cluster_accuracy.csv", output: - accuracies="docs/figures/flu-2018-2020-replication-of-cluster-accuracy.png", + accuracies="manuscript/figures/flu-2018-2020-replication-of-cluster-accuracy.png", conda: "../cartography.yml" notebook: "../notebooks/plot-replication-of-cluster-accuracy.py.ipynb" diff --git a/seasonal-flu-nextstrain/Snakefile b/seasonal-flu-nextstrain/Snakefile index 59a24350..3bad4108 100644 --- a/seasonal-flu-nextstrain/Snakefile +++ b/seasonal-flu-nextstrain/Snakefile @@ -1,12 +1,12 @@ rule seasonal_flu_training: input: - "docs/figures/flu-2016-2018-ha-embeddings-by-clade.png", - "docs/figures/flu-2016-2018-ha-embeddings-by-clade.html", - "docs/figures/flu-2016-2018-ha-euclidean-distance-by-genetic-distance.png", - "docs/figures/flu-2016-2018-ha-embeddings-by-cluster.png", - "docs/figures/flu-2016-2018-ha-embeddings-by-cluster.html", - "docs/figures/flu-2016-2018-mds-by-clade.html", - "docs/figures/flu-2016-2018-mds-by-clade.png", + "manuscript/figures/flu-2016-2018-ha-embeddings-by-clade.png", + "manuscript/figures/flu-2016-2018-ha-embeddings-by-clade.html", + "manuscript/figures/flu-2016-2018-ha-euclidean-distance-by-genetic-distance.png", + "manuscript/figures/flu-2016-2018-ha-embeddings-by-cluster.png", + "manuscript/figures/flu-2016-2018-ha-embeddings-by-cluster.html", + "manuscript/figures/flu-2016-2018-mds-by-clade.html", + "manuscript/figures/flu-2016-2018-mds-by-clade.png", "auspice/cartography_flu-seasonal-h3n2-ha-2016-2018.json", "seasonal-flu-nextstrain/results/mutation_table.csv", "seasonal-flu-nextstrain/results/full_within_between_stats.csv" @@ -689,7 +689,7 @@ rule seasonal_flu_training_create_scatterplot_figure: scatterplot_tsne = "seasonal-flu-nextstrain/results/scatterplot_t-sne.csv", scatterplot_umap = "seasonal-flu-nextstrain/results/scatterplot_umap.csv", output: - scatterplot = "docs/figures/flu-2016-2018-ha-euclidean-distance-by-genetic-distance.png", + scatterplot = "manuscript/figures/flu-2016-2018-ha-euclidean-distance-by-genetic-distance.png", conda: "../cartography.yml" notebook: "../notebooks/2022-09-26-scatterplot-figure.py.ipynb" @@ -701,12 +701,12 @@ rule seasonal_flu_training_create_notebook_docs: accuracy_table="seasonal-flu-nextstrain/results/optimal_cluster_accuracy_and_parameters.csv", explained_variance_pca="seasonal-flu-nextstrain/results/explained_variance_pca_sequences.csv", output: - fullChartPNG = "docs/figures/flu-2016-2018-ha-embeddings-by-clade.png", - fullChart = "docs/figures/flu-2016-2018-ha-embeddings-by-clade.html", - fullChartHDBSCANPNG = "docs/figures/flu-2016-2018-ha-embeddings-by-cluster.png", - fullChartHDBSCAN = "docs/figures/flu-2016-2018-ha-embeddings-by-cluster.html", - MDS_Supplement = "docs/figures/flu-2016-2018-mds-by-clade.html", - MDS_Supplement_PNG = "docs/figures/flu-2016-2018-mds-by-clade.png", + fullChartPNG = "manuscript/figures/flu-2016-2018-ha-embeddings-by-clade.png", + fullChart = "manuscript/figures/flu-2016-2018-ha-embeddings-by-clade.html", + fullChartHDBSCANPNG = "manuscript/figures/flu-2016-2018-ha-embeddings-by-cluster.png", + fullChartHDBSCAN = "manuscript/figures/flu-2016-2018-ha-embeddings-by-cluster.html", + MDS_Supplement = "manuscript/figures/flu-2016-2018-mds-by-clade.html", + MDS_Supplement_PNG = "manuscript/figures/flu-2016-2018-mds-by-clade.png", conda: "../cartography.yml" notebook: "2022-03-29-final-figures.py.ipynb" diff --git a/simulations/Snakefile b/simulations/Snakefile index 37b90e35..55b8a86a 100644 --- a/simulations/Snakefile +++ b/simulations/Snakefile @@ -243,7 +243,7 @@ rule simulations_summarize_grid_search: mds_parameters = "simulations/{virus}-like/{recombination_rate}/mds_parameters.csv", tsne_parameters = "simulations/{virus}-like/{recombination_rate}/t-sne_parameters.csv", umap_parameters = "simulations/{virus}-like/{recombination_rate}/umap_parameters.csv", - scores_by_parameters = "docs/figures/simulated-{virus}-like-with-{recombination_rate}-scores-by-parameters.png", + scores_by_parameters = "manuscript/figures/simulated-{virus}-like-with-{recombination_rate}-scores-by-parameters.png", summary_score_by_method = "simulations/{virus}-like/{recombination_rate}/summary_scores_by_method.csv", conda: "../cartography.yml" log: @@ -429,8 +429,8 @@ rule simulations_representative_plot: coronavirus_tsne="simulations/coronavirus-like/moderate-recombination-rate/replicate-4/representative/embed_t-sne.csv", coronavirus_umap="simulations/coronavirus-like/moderate-recombination-rate/replicate-4/representative/embed_umap.csv", output: - all_embeddings="docs/figures/simulated-populations-representative-embeddings.png", - mds_embeddings="docs/figures/simulated-populations-representative-mds-embeddings.png", + all_embeddings="manuscript/figures/simulated-populations-representative-embeddings.png", + mds_embeddings="manuscript/figures/simulated-populations-representative-mds-embeddings.png", conda: "../cartography.yml" log: "logs/simulations_representative_plot.py.ipynb"