From 6e8f7ef4f49d49cc06e66c0c463f72a29ae5640e Mon Sep 17 00:00:00 2001 From: Michael-Geuenich Date: Fri, 2 Jun 2023 01:06:47 -0400 Subject: [PATCH] update environment --- Pipfile | 1 + Pipfile.lock | 1235 ++++++++++++++++++++++++++++++++++++ pipeline/paper-figures.smk | 126 ++++ run_snakemake.sh | 2 + 4 files changed, 1364 insertions(+) create mode 100644 Pipfile.lock create mode 100644 pipeline/paper-figures.smk create mode 100755 run_snakemake.sh diff --git a/Pipfile b/Pipfile index eeb7d2e..477b85b 100644 --- a/Pipfile +++ b/Pipfile @@ -6,6 +6,7 @@ name = "pypi" [packages] snakemake = "*" deeptools = "*" +numpy = "*" [dev-packages] diff --git a/Pipfile.lock b/Pipfile.lock new file mode 100644 index 0000000..27fe054 --- /dev/null +++ b/Pipfile.lock @@ -0,0 +1,1235 @@ +{ + "_meta": { + "hash": { + "sha256": "b222c6d3ff0311b016b6be0b96a35774d4473808ca82ca04432e13baf1250d4b" + }, + "pipfile-spec": 6, + "requires": { + "python_version": "3.8" + }, + "sources": [ + { + "name": "pypi", + 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/dev/null +++ b/pipeline/paper-figures.smk @@ -0,0 +1,126 @@ + +final_figures = { + 'fig1': output + "paper-figures/figure1.pdf", + 'fig2': output + "paper-figures/lr-and-rf-heatmaps.pdf", + 'fig3_imb': output + "paper-figures/imbalance-main-figure.pdf", + 'fig3_acc': output + "paper-figures/overall-accuracies.pdf", + 'fig4': output + "paper-figures/rem-cell-type.pdf", + 'fig5': output + "paper-figures/pred-labelling.pdf", +} + +# Figure 1 +rule benchmarking_overview: + input: + cytof = "data/CyTOF/CyTOF-full.rds", + scrna = "data/scRNASeq/scRNASeq-full.rds", + snrna = "data/snRNASeq/snRNASeq-full.rds", + schematic = "illustrator-figures/benchmarking-schematic.ai" + output: + fig1 = output + "paper-figures/figure1.pdf" + script: + "figures/figure1.R" + +# Figure 2 +rule rf_vs_lr_and_ranking_vs_random: + input: + cytof = "data/CyTOF/CyTOF-train-seed-0.rds", + cytof_AL_rand = expand(output + "data/CyTOF/Active-Learning_entropy/AL-batches-subset/Init_random-strat-highest_entropy-ALAlg-rf-rand_sel-0-corr-0-knn_neighbors-NA-resolution-NA-seed-{s}-100_cells.tsv", s = train_test_seeds), + cytof_AL_rank = expand(output + "data/CyTOF/Active-Learning_entropy/AL-batches-subset/Init_ranking-strat-highest_entropy-ALAlg-rf-rand_sel-0-corr-0-knn_neighbors-NA-resolution-NA-seed-{s}-100_cells.tsv", s = train_test_seeds), + scrna = "data/scRNASeq/scRNASeq-train-seed-0.rds", + scrna_AL_rand = expand(output + "data/scRNASeq/Active-Learning_entropy/AL-batches-subset/Init_random-strat-highest_entropy-ALAlg-rf-rand_sel-0-corr-0-knn_neighbors-NA-resolution-NA-seed-{s}-100_cells.tsv", s = train_test_seeds), + scrna_AL_rank = expand(output + "data/scRNASeq/Active-Learning_entropy/AL-batches-subset/Init_ranking-strat-highest_entropy-ALAlg-rf-rand_sel-0-corr-0-knn_neighbors-NA-resolution-NA-seed-{s}-100_cells.tsv", s = train_test_seeds), + snrna = "data/snRNASeq/snRNASeq-train-seed-0.rds", + snrna_AL_rand = expand(output + "data/scRNASeq/Active-Learning_entropy/AL-batches-subset/Init_random-strat-highest_entropy-ALAlg-rf-rand_sel-0-corr-0-knn_neighbors-NA-resolution-NA-seed-{s}-100_cells.tsv", s = train_test_seeds), + snrna_AL_rank = expand(output + "data/scRNASeq/Active-Learning_entropy/AL-batches-subset/Init_ranking-strat-highest_entropy-ALAlg-rf-rand_sel-0-corr-0-knn_neighbors-NA-resolution-NA-seed-{s}-100_cells.tsv", s = train_test_seeds), + accs = expand(output + "results/overall-{mod}-benchmarking-accuracies.tsv", mod = modalities) + output: + rank_rand_hm = output + "paper-figures/ranking-random-heatmap.pdf", + lr_rf_hm = output + "paper-figures/lr-rf-heatmap.pdf", + main_fig = output + "paper-figures/lr-and-rf-heatmaps.pdf", + rf_lr_supp = output + "paper-figures/rf-vs-lr-supplementary.pdf", + rand_rank_supp = output + "paper-figures/random-vs-ranking-supplementary.pdf" + script: + "figures/compare-lr-rf-random-and-ranking.R" + +# Figure 3 +rule imbalance_plot: + input: + cytof_acc = output + "imbalance/acc/imbalance-acc-CyTOF.tsv", + scrna_acc = output + "imbalance/acc/imbalance-acc-scRNASeq.tsv", + snrna_acc = output + "imbalance/acc/imbalance-acc-snRNASeq.tsv" + output: + main_fig = output + "paper-figures/imbalance-main-figure.pdf", + sup_fig = output + "paper-figures/imbalance-supplementary.pdf" + script: + "figures/imbalance-plots.R" + +rule overall_acc: + input: + accs = expand(output + "results/overall-{mod}-benchmarking-accuracies.tsv", mod = modalities), + output: + overall_fig = output + "paper-figures/overall-accuracies.pdf" + script: + "figures/figure3.R" + + +# Figure 4 +rule rem_cell_types: + input: + scrna = expand(output + "results/rem_cell_type/Init-sel-random-rem-{cell_line}-scRNASeq-highest_entropy-ALAlg-{al}-cell_num-20-seed-{s}.tsv", cell_line = ['JIMT1', 'AU565'], al = ['multinom', 'rf'], s = train_test_seeds), + snrna = expand(output + "results/rem_cell_type/Init-sel-random-rem-{cell_type}-snRNASeq-highest_entropy-ALAlg-multinom-cell_num-20-seed-{s}.tsv", cell_type = ['Ductal', 'Endothelial', 'Schwann'], s = train_test_seeds), + snrna_group = expand(output + "results/rem_cell_type/Init-sel-random-rem-schwann_l1-snRNASeq-highest_entropy-ALAlg-multinom-cell_num-20-seed-{s}.tsv", s = train_test_seeds), + cytof = expand(output + "results/rem_cell_type/Init-sel-random-rem-{cell_type}-CyTOF-highest_entropy-ALAlg-multinom-cell_num-20-seed-{s}.tsv", cell_type = ['Classical Monocytes', 'CD8 T cells'], s = train_test_seeds), + snrna_supp = expand(output + "results/rem_cell_type/Init-sel-random-rem-{cell_type}-snRNASeq-highest_entropy-ALAlg-rf-cell_num-20-seed-{s}.tsv", cell_type = ['Ductal', 'Endothelial', 'Schwann'], s = train_test_seeds), + snrna_supp_group = expand(output + "results/rem_cell_type_group/Init-sel-random-rem-schwann_l1-snRNASeq-highest_entropy-ALAlg-rf-cell_num-20-seed-{s}.tsv", s = train_test_seeds), + cytof_supp = expand(output + "results/rem_cell_type/Init-sel-random-rem-{cell_type}-CyTOF-highest_entropy-ALAlg-rf-cell_num-20-seed-{s}.tsv", cell_type = ['Classical Monocytes', 'CD8 T cells'], s = train_test_seeds), + output: + main = output + "paper-figures/rem-cell-type.pdf", + supp = output + "paper-figures/supp-rem-cell-type.pdf" + script: + "figures/rem-cell-type.R" + +# Figure 5 +rule self_training: + input: + acc = output + "new/pred-labeling-accuracy.tsv", + scrna = output + "new/pred2/benchmark-predictive-labeling-scRNASeq.tsv", + snrna = output + "new/pred2/benchmark-predictive-labeling-snRNASeq.tsv", + cytof = output + "new/pred2/benchmark-predictive-labeling-CyTOF.tsv", + mislabelled_cytof = expand(output + "identify_mislabelled/CyTOF/Pred_alg-{al}-corr-10-seed-{s}-cellNum-250-cells.tsv", al = ['rf', 'multinom'], s = train_test_seeds), + mislabelled_scrna = expand(output + "identify_mislabelled/scRNASeq/Pred_alg-{al}-corr-10-seed-{s}-cellNum-250-cells.tsv", al = ['rf', 'multinom'], s = train_test_seeds), + mislabelled_snrna = expand(output + "identify_mislabelled/snRNASeq/Pred_alg-{al}-corr-10-seed-{s}-cellNum-250-cells.tsv", al = ['rf', 'multinom'], s = train_test_seeds), + output: + supp = output + "paper-figures/Supp-pred-labelling-acc.pdf", + main = output + "paper-figures/pred-labelling.pdf", + sup_cytof = output + "paper-figures/Supp-CyTOF-f1-improvement.pdf", + sup_scrna = output + "paper-figures/Supp-scRNASeq-f1-improvement.pdf", + sup_snrna = output + "paper-figures/Supp-snRNASeq-f1-improvement.pdf" + script: + "figures/pred-labelling.R" + + +#### Supplemental figs +# similarity fig +rule cell_type_sim: + input: + cytof_sim = output + "results/cell-type-similarity/similarity-CyTOF-seed-0.tsv", + scrna_sim = output + "results/cell-type-similarity/similarity-scRNASeq-seed-0.tsv", + snrna_sim = output + "results/cell-type-similarity/similarity-snRNASeq-seed-0.tsv" + output: + scrna = output + "paper-figures/Supp-cell-type-sim-scRNASeq.pdf", + snrna = output + "paper-figures/Supp-cell-type-sim-snRNASeq.pdf", + cytof = output + "paper-figures/Supp-cell-type-sim-CyTOF.pdf" + script: + "figures/cell-type-similarity.R" + +# ar params +rule AR_params: + input: + cytof_acc = output + "results/overall-CyTOF-benchmarking-accuracies.tsv", + scrna_acc = output + "results/overall-scRNASeq-benchmarking-accuracies.tsv", + snrna_acc = output + "results/overall-snRNASeq-benchmarking-accuracies.tsv" + output: + res = output + "paper-figures/Supp-AR-res.pdf", + knn = output + "paper-figures/Supp-AR-knn.pdf" + script: + "figures/AR-params.R" \ No newline at end of file diff --git a/run_snakemake.sh b/run_snakemake.sh new file mode 100755 index 0000000..93f453d --- /dev/null +++ b/run_snakemake.sh @@ -0,0 +1,2 @@ +#!/bin/sh +snakemake --profile slurm -j 500 --rerun-triggers mtime --rerun-incomplete