MS_figures_src

Ortho2tree manuscript figure/plot files

(3-March-2024)

This folder contains all of the datafiles and .R code to recreate the figures in the manuscript: Improved selection of canonical proteins for reference proteomes.

To recreate pdf files for the figures, run: plot_MS_pub.sh

Each .R script has an associated figure number associated with it. fig1_percid_gaps3.R is used for Fig. 1 and Suppl. Fig. 4. In addition, several of the scripts use set_color_a90.R to set line types, symbols, and colors.

In addition to the .R scripts to create the files, various data files are included:

• aln_data/ contains *.summ2i and *.summ2i_m files that report the best hits for various search runs. For example, human_vs_mam_canon.summ2i contains the best hits for the searches of human canonical proteins vs gorgo (gorilla), mouse, rat, bovin, and mondo (opossum) reference proteomes. *.summ2i files are plotted by fig1_percid_gaps3.R for Fig. 1 and suppl. Fig. 4. aln_data/*.summ2i_m are derived from *.summ2i files, but have an an additional file that indicates the Panther orthogroup for the human (or mouse) query. These files are used by fig5_percid_gaps6.R.

• cnt_data/ contains a set of .tab files that report the clade sizes for each of the orthogroups for a specific UniProtKB release, used in Fig. 7. Thus, mam2023_01_clade_stats2.tab contains the clade sizes for the proposed changes made starting with the UP2023_01 release set. The Trembl/Trembl proposed changes from this analysis were actually incorporated into the UP2023_02 release. The ortho2tree changes were proposed based on the 8 QfO mammals in release UP2022_05; the qfomam_2022_05_clade_stats2.tab file has the clade size statistics for that analysis (which was actually incorporated into UP release 2023_01, the first release using ortho2tree suggestions).

Note that these folders are compressed as .tar.gz archives, and will be uncompressed when running the script plot_MS_pub.sh

Other data files include:

• qfomam_output_changes240206.one and qfomam_output_confirm240206, used to create Suppl. Fig. 1

• pmam2023_05_output_gc211004 used to create Suppl. Fig 3

• history_new_changes_by_species.tsv used to create Fig. 6

• *.times -- files that provide the divergence times used in Figs. 1 and Suppl. Fig. 4