This repo contains code meant to facilitate reproduction of the analyses in Mah & Dunn (2023), Reconstructing cell type evolution across species through cell phylogenies of single-cell RNAseq data.
Link to bioRxiv: https://www.biorxiv.org/content/10.1101/2023.05.18.541372v2
First run the file containing all functions used in the analyses: cellphylo_functions.R. SessionInfo can be found in sessionInfo_R.txt.
All analyses can be replicated in full by running these notesbooks in the analysis directory, in order:
1_Wrangle_Data.Rmd: Format matrices into cellphylo format
2_Create_Matrices.Rmd: Create the within and cross-species integrated matrices (Fig. S1 steps 1-6)
3_PC_sweep_analysis.Rmd: Perform the PC sweep analysis (Figure 2)
4_Jumble_analysis.Rmd: Infer the focal tree for Figure 4 and calculate jumble scores.
5_scJackknife_analysis.Rmd: Calculate scjackknife scores for the tree in Figure 4.
6_Average_cells.Rmd: Infer the focal tree for Figure 5 and calculate jumble and scjackknife scores.
7_GO_and_phenetic_trees.Rmd: Perform the GO enrichment analysis (Table 1, S1, S6) and calculate the phenetic trees (Figs. S7-S10).
Select input, intermediate and output files sufficient for reproduction of the analyses have been provided have in the analysis directory. A thorough description of each of these files is provided in the notebooks as they walk through the analysis.
A brief description of folders of cellphylo/analysis:
analysis/
├── 1_Wrangle_Data.Rmd
├── 2_Create_Matrices.Rmd
├── 3_PC_sweep_analysis.Rmd
├── 4_Jumble_analysis.Rmd
├── 5_scJackknife_analysis.Rmd
├── 6_Average_cells.Rmd
├── 7_GO_and_phenetic_trees.Rmd
├── GO_enrichment
│ └── PCA_919x919_matrix.rds
├── PC_sweep
│ ├── input
│ │ └── pc_sweep_infiles_final.tar.gz
│ └── output
│ └── pc_sweep_919_outtrees.tar.gz
├── ann
│ ├── AqHumor_ensembl_orthologs.txt
│ └── all_five_species_metafile.csv
├── average
│ ├── 540_cell_subset_cell_ids.txt
│ ├── booster
│ │ ├── multiphylo_scjack_means_5reps_540_common_label.tre
│ │ ├── outtree_54mean_20PC_afterPCA_jumble_search_2525674179_common_label.tre
│ │ └── outtree_54mean_20PC_afterPCA_jumble_search_2525674179_common_label_best_tree_TBE.tre
│ ├── jumble
│ │ ├── input
│ │ │ ├── contml_54means_20PC_afterPCA_mtx
│ │ │ │ ├── barcodes.tsv.gz
│ │ │ │ ├── features.tsv.gz
│ │ │ │ └── matrix.mtx.gz
│ │ │ └── infile_54means_20PC_afterPCA
│ │ └── output
│ │ ├── 54mean_20PC_afterPCA_jumble_search_2525674179_scored_label.tre
│ │ └── outtrees_54mean_20PC_afterPCA_jumble_search_processed.tar.gz
│ └── scjackknife
│ ├── input
│ │ └── input_540_cells_20PC_after_PCA.tar.gz
│ └── output
│ └── output_processed
│ ├── errored_runs_mean.txt
│ ├── outtree_scjack_means_5reps_540_common_label.tar.gz
│ ├── outtrees_scjack_means_5reps_540_processed.tar.gz
│ └── scjack_matrices_processed.tar.gz
├── goseq_positive_BP_PC20_enriched.txt
├── jumble
│ ├── input
│ │ ├── contml_54cell_subset_pca_var_norm_20PC_mtx
│ │ │ ├── barcodes.tsv.gz
│ │ │ ├── features.tsv.gz
│ │ │ └── matrix.mtx.gz
│ │ └── infile_54_20PC
│ └── output
│ ├── outtree_54_jumble_search_1249177875_scored_label.tre
│ └── outtrees_54_jumble_search_processed.tar.gz
├── matrix
│ ├── cross-species_integration
│ │ ├── aqhumor_cross_species_92_subset.txt
│ │ └── aqhumor_cross_species_integrated_mtx
│ │ ├── barcodes.tsv.gz
│ │ ├── features.tsv.gz
│ │ └── matrix.mtx.gz
│ └── subset
│ ├── integrated_subset_mtx_human
│ │ ├── barcodes.tsv.gz
│ │ ├── features.tsv.gz
│ │ └── matrix.mtx.gz
│ ├── integrated_subset_mtx_macF
│ │ ├── barcodes.tsv.gz
│ │ ├── features.tsv.gz
│ │ └── matrix.mtx.gz
│ ├── integrated_subset_mtx_macM
│ │ ├── barcodes.tsv.gz
│ │ ├── features.tsv.gz
│ │ └── matrix.mtx.gz
│ ├── integrated_subset_mtx_mouse
│ │ ├── barcodes.tsv.gz
│ │ ├── features.tsv.gz
│ │ └── matrix.mtx.gz
│ └── integrated_subset_mtx_pig
│ ├── barcodes.tsv.gz
│ ├── features.tsv.gz
│ └── matrix.mtx.gz
├── phenetic_trees
│ ├── 54_means_pca_var_norm_20_PC_nj.tre
│ ├── 54_means_pca_var_norm_20_PC_upgma.tre
│ ├── 54_means_pca_var_norm_20_PC_wpgma_mcquitty.tre
│ └── NJ_scjack_analysis
│ ├── booster
│ │ └── multiphylo_nj_means_outtrees_scjack_540_TBE_common_label.tre
│ ├── output
│ │ ├── nj_means_outtrees_scjack_540_TBE_common_label.tar.gz
│ │ └── nj_trees_means_scjack_540.tar.gz
│ └── scored_trees
│ └── 54_means_BM_with_NJ_multiphylo.tre
├── scjackknife
│ ├── booster
│ │ ├── multiphylo_scjack_540_TBE_common_label.tre
│ │ ├── outtree_54_jumble_search_1249177875_common_label.tre
│ │ └── outtree_54_jumble_search_1249177875_scored_with_scjack540TBE.tre
│ ├── contml_919cell_subset_20PC_mtx
│ │ ├── barcodes.tsv.gz
│ │ ├── features.tsv.gz
│ │ └── matrix.mtx.gz
│ ├── input
│ │ └── input_scjack_540_TBE.tar.gz
│ ├── matrix_540cell_cross_species_integrated_mtx
│ │ ├── barcodes.tsv.gz
│ │ ├── features.tsv.gz
│ │ └── matrix.mtx.gz
│ └── output
│ └── output_processed
│ ├── errored_runs.txt
│ ├── outtrees_scjack_540_TBE_common_label.tar.gz
│ ├── outtrees_scjack_540_TBE_processed.tar.gz
│ └── scjack_matrices_processed.tar.gz
├── scripts
│ ├── PC_sweep
│ │ └── contml_pc_sweep_919.sh
│ ├── average
│ │ ├── jumble
│ │ │ ├── run_jumble_parallel_54mean_20PC_afterPCA.sh
│ │ │ └── script_jumble_parallel_54mean_20PC_afterPCA.sh
│ │ ├── lsi
│ │ └── scjack
│ │ ├── in_script_scjack_parallel_means_5reps_540.sh
│ │ ├── make_reps_scjack_means_5reps_540.sh
│ │ ├── run_scjack_parallel_means_5reps_540.sh
│ │ └── scjack_scripts_mean.tar.gz
│ ├── jumble
│ │ ├── run_jumble_parallel_54.sh
│ │ └── script_jumble_parallel_54.sh
│ └── scjackknife
│ ├── in_script_scjack_parallel_540_TBE.sh
│ ├── make_reps_scjack_540_TBE.sh
│ ├── run_scjack_parallel_540_TBE.sh
│ └── scjack_scripts.tar.gz
└── tree_inference
├── 54_cell_tree
│ └── contml_54cell_subset_pca_var_norm_20PC_mtx
│ ├── barcodes.tsv.gz
│ ├── features.tsv.gz
│ └── matrix.mtx.gz
└── 92_cell_tree
├── aqhumor_cross_species_92_subset.txt
└── contml_92cell_subset_pca_var_norm_20PC_mtx
├── barcodes.tsv.gz
├── features.tsv.gz
└── matrix.mtx.gz
54 directories, 94 files
Additional supplementary files referenced in the text are provided in cellphylo/supplementary_files/
Mah, J.L., and Dunn, C.W. Reconstructing cell type evolution across species through cell phylogenies of single-cell RNAseq data. bioRxiv, (2023).
Updated August 31 2023