R/doubledeepms.R
In lehner-lab/doubledeepms: Analysis scripts to reproduce the figures and results from doubleDeepPCA manuscript
Defines functions
doubledeepms
Documented in
doubledeepms
#' doubledeepms
#'
#' Main analysis script.
#'
#' @param startStage Start at a specified analysis stage (default:1)
#' @param stopStage Stop at a specified analysis stage (default:15)
#' @param base_dir Base directory for all output files (default:NB private CRG server path; change accordingly)
#' @param tmodel_job_number Thermodynamic model fit job number: 1:final model, 2-11: monte carlo simluations for confidence intervals of model-inferred free energies (default:1)
#' @param tmodel_grid_search Thermodynamic model fit grid search to determine optimal hyperparameters (default:FALSE)
#' @param tmodel_protein Thermodynamic model fit proteins: comma-separated list of names or 'all' (default:'GRB2-SH3')
#' @param tmodel_subset Thermodynamic model fit data subset: either an integer percentage of subsampled doubles (1-100) or "binding_only" or "singles_only" (default:100)
#'
#' @return Nothing
#' @export
doubledeepms <- function(
startStage = 1,
stopStage = 15,
base_dir = "/users/project/prj004631/afaure/DMS/Results/doubledeepms_proj",
tmodel_job_number = 1,
tmodel_grid_search = FALSE,
tmodel_protein = "GRB2-SH3",
tmodel_subset = 100
){
# startStage=1
# stopStage=15
# base_dir = "/users/project/prj004631/afaure/DMS/Results/doubledeepms_proj"
# rerun_raw = F
colour_scheme <- list(
"shade 0" = list(
"#F4270C",
"#F4AD0C",
"#1B38A6",
"#09B636"),
"shade 1" = list(
"#FFB0A5",
"#FFE4A5",
"#9DACE3",
"#97E9AD"),
"shade 2" = list(
"#FF6A56",
"#FFCB56",
"#4C63B7",
"#43C766"),
"shade 3" = list(
"#A31300",
"#A37200",
"#0C226F",
"#007A20"),
"shade 4" = list(
"#410800",
"#412D00",
"#020B2C",
"#00300D"),
"shade 5" = list(
"#CCCCCC",
"#FF991F",
"#5CB8FF",
"#B22222"
))
#First and last analysis stages
first_stage <- startStage
last_stage <- stopStage
### Fit thermo models
###########################
stagenum <- 0
doubledeepms_fit_thermo_model(
base_dir = base_dir,
tmodel_job_number = tmodel_job_number,
tmodel_grid_search = tmodel_grid_search,
tmodel_protein = tmodel_protein,
tmodel_subset = as.character(tmodel_subset),
tmodel_hyperparameters = file.path(base_dir, "Data", "mochi", "hyperparameters.txt"),
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Evaluate thermo model results
###########################
stagenum <- 1
#GB1
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 2%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample2p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample2p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 5%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample5p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample5p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 10%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample10p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample10p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 20%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample20p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample20p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 50%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample50p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample50p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - binding only
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_bindingonly"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3bindingonly", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - singles only
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_singlesonly"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3singlesonly", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 2%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample2p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample2p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 5%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample5p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample5p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 10%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample10p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample10p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 20%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample20p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample20p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 50%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample50p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample50p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - binding only
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_bindingonly"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3bindingonly", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - singles only
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_singlesonly"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3singlesonly", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 2%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample2p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample2p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 5%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample5p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample5p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 10%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample10p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample10p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 20%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample20p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample20p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 50%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample50p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample50p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Add 3D structure metrics
###########################
stagenum <- 2
#GB1
doubledeepms_structure_metrics(
input_file = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_GB1"), "dg_singles.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_structure_metrics_GB1", stagenum=stagenum, base_dir=base_dir),
pdb_file = file.path(base_dir, "Data", "pdb", "1fcc.pdb"),
pdb_chain_query = "C",
pdb_chain_target = "A",
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_structure_metrics(
input_file = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_PSD95-PDZ3"), "dg_singles.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_structure_metrics_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
pdb_file = file.path(base_dir, "Data", "pdb", "1be9.pdb"),
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_structure_metrics(
input_file = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_GRB2-SH3"), "dg_singles.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_structure_metrics_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
pdb_file = file.path(base_dir, "Data", "pdb", "2vwf.pdb"),
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Fitness plots
###########################
stagenum <- 3
#PSD95-PDZ3 and GRB2-SH3
doubledeepms_fitness_plots(
fitness_list = list(
"GB1" = file.path(base_dir, "Data", "fitness", "GB1"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "fitness", "PSD95-PDZ3"),
"GRB2-SH3" = file.path(base_dir, "Data", "fitness", "GRB2-SH3")),
structure_metrics_list = list(
"GB1" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
"PSD95-PDZ3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
"GRB2-SH3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt")),
val_inpath = file.path(base_dir, "Data", "experimental_validations", "GRB2-SH3", "experimenal_validations_ODs.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_fitness_plots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Plot fitness heatmaps
###########################
stagenum <- 4
#GB1
doubledeepms_fitness_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
input_file_fitness = file.path(base_dir, "Data", "fitness", "GB1"),
domain_name = "GB1",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_fitness_heatmaps_GB1", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 11,
plot_traits = "Binding",
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_fitness_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
input_file_fitness = file.path(base_dir, "Data", "fitness", "PSD95-PDZ3"),
input_file_MSA = file.path(base_dir, "Data", "MSA", "PSD95-PDZ3", "frequencies.csv"),
domain_name = "PSD95 PDZ3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_fitness_heatmaps_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 15,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_fitness_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt"),
input_file_fitness = file.path(base_dir, "Data", "fitness", "GRB2-SH3"),
input_file_MSA = file.path(base_dir, "Data", "MSA", "GRB2-SH3", "frequencies.csv"),
domain_name = "GRB2 SH3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_fitness_heatmaps_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 11,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Plot free energy scatterplots
###########################
stagenum <- 5
#All domains
doubledeepms_free_energy_scatterplots(
input_list = list(
"GB1" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
"PSD95-PDZ3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
"GRB2-SH3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt")),
input_MSA_list = list(
"GB1" = file.path(base_dir, "Data", "MSA", "GB1", "frequencies.csv"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "MSA", "PSD95-PDZ3", "frequencies.csv"),
"GRB2-SH3" = file.path(base_dir, "Data", "MSA", "GRB2-SH3", "frequencies.csv")
),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_free_energy_scatterplots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Plot free energy heatmaps
###########################
stagenum <- 6
#GB1
doubledeepms_free_energy_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
domain_name = "GB1",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_free_energy_heatmaps_GB1", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 11,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_free_energy_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
domain_name = "PSD95 PDZ3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_free_energy_heatmaps_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 15,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_free_energy_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt"),
domain_name = "GRB2 SH3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_free_energy_heatmaps_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 11,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Protein stability plots
###########################
stagenum <- 7
#All domains
doubledeepms_protein_stability_plots(
input_list = list(
"GB1" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
"PSD95-PDZ3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
"GRB2-SH3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt")),
pdb_file_list = list(
"GB1" = file.path(base_dir, "Data", "pdb", "1fcc.pdb"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "pdb", "1be9.pdb"),
"GRB2-SH3" = file.path(base_dir, "Data", "pdb", "2vwf.pdb")),
pdb_chain_query_list = list(
"GB1" = "C",
"PSD95-PDZ3" = "A",
"GRB2-SH3" = "A"),
aaprop_file = file.path(base_dir, "Data", "amino_acid_properties", "amino_acid_properties_annotated_supplementary.txt"),
aaprop_file_selected = file.path(base_dir, "Data", "amino_acid_properties", "selected.amino_acid_properties.txt"),
input_MSA_list = list(
"GB1" = file.path(base_dir, "Data", "MSA", "GB1", "frequencies.csv"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "MSA", "PSD95-PDZ3", "frequencies.csv"),
"GRB2-SH3" = file.path(base_dir, "Data", "MSA", "GRB2-SH3", "frequencies.csv")
),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_protein_stability_plots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Binding interface plots
###########################
stagenum <- 8
# GRB2-SH3
doubledeepms_interface_mechanisms(
base_dir = base_dir,
domain_name = "GRB2-SH3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_ligand_interface_plots", stagenum=stagenum, base_dir=base_dir),
mut_subset_list = list(
c("T", "F","Q","H", "S", "V", "I", "C"),
c("T", "S", "L", "V", "A", "K", "R")),
pos_subset_list = list(
c(7, 51),
c(46)),
ligand_pos_list = list(
c(3,4),
c(11)),
pdb_id = "2vwf",
pdb_view = "(0.837024331,0.261427671,0.480670929,0.209657252,0.658192515,-0.723066926,-0.505404055,0.706001341,0.496113181,0.000000000,0.000000000,-141.782043457,-2.309909821,13.775757790,0.139801025,111.782043457,171.782043457,-20.000000000 )",
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
# All domains
doubledeepms_binding_interface(
input_list = list(
"GB1" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
"PSD95-PDZ3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
"GRB2-SH3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_binding_interface", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Allostery plots
###########################
stagenum <- 9
#All domains
doubledeepms_allostery_plots(
input_file = file.path(base_dir, paste0("007", "_doubledeepms_protein_stability_plots"), "dg_singles.txt"),
pdb_file_list = list(
"GB1" = file.path(base_dir, "Data", "pdb", "1fcc.pdb"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "pdb", "1be9.pdb"),
"GRB2-SH3" = file.path(base_dir, "Data", "pdb", "2vwf.pdb")),
pdb_chain_query_list = list(
"GB1" = "C",
"PSD95-PDZ3" = "A",
"GRB2-SH3" = "A"),
annotation_list = list(
"PSD95-PDZ3" = file.path(base_dir, "Data", "annotations", "PSD95-PDZ3", "PSD95-PDZ3_annotations.txt")),
ohm_file_list = list(
"GB1" = file.path(base_dir, "Data", "ohm", "ohm_2gb1_ddPCA_GB1only.txt"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "ohm", "ohm_1be9_ddPCA_PDZonly.txt"),
"GRB2-SH3" = file.path(base_dir, "Data", "ohm", "ohm_2vwf_ddPCA_GRB2only.txt")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_allostery_plots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Allostery scatterplots
###########################
stagenum <- 10
#All domains
doubledeepms_allostery_scatterplots(
input_file = file.path(base_dir, paste0("009", "_doubledeepms_allostery_plots"), "dg_singles.txt"),
fitness_list = list(
"PSD95-PDZ3" = file.path(base_dir, "Data", "fitness", "PSD95-PDZ3"),
"GRB2-SH3" = file.path(base_dir, "Data", "fitness", "GRB2-SH3")),
mochi_outpath_list = list(
"PSD95-PDZ3" = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128"),
"GRB2-SH3" = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_allostery_scatterplots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Downsampling analysis
###########################
stagenum <- 11
#GB1
doubledeepms_downsampling_analysis(
mochi_outpath_prefix = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample"),
sample_percentage = c(2, 5, 10, 20, 50, 100),
literature_comparison_prefix = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_GB1subsample")),
literature_comparison_list = list(
"folding" = "validation_scatter_(mAvg)_mean_f_ddg_conf.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_downsampling_analysis_GB1", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_downsampling_analysis(
mochi_outpath_prefix = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample"),
sample_percentage = c(2, 5, 10, 20, 50, 100),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_downsampling_analysis_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_downsampling_analysis(
mochi_outpath_prefix = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample"),
sample_percentage = c(2, 5, 10, 20, 50, 100),
literature_comparison_prefix = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_PSD95-PDZ3subsample")),
literature_comparison_list = list(
"folding" = "validation_scatter_Calosci_2008_f_ddg_conf.txt",
"binding" = "validation_scatter_Laursen_2020_b_ddg_conf.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_downsampling_analysis_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Foldx comparisons
###########################
stagenum <- 12
#All domains
doubledeepms_foldx_comparisons(
input_file = file.path(base_dir, paste0("009", "_doubledeepms_allostery_plots"), "dg_singles.txt"),
foldx_file_list = list(
"GB1" = file.path(base_dir, "Data", "foldx", "GB1", "PS_2gb1_nowater_noligand_restrict_scanning_output.txt"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "foldx", "PSD95-PDZ3", "PS_1be9_nowater_noligand_restrict_scanning_output.txt"),
"GRB2-SH3" = file.path(base_dir, "Data", "foldx", "GRB2-SH3", "PS_2vwf_nowater_noligand_restrict_scanning_output.txt")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_foldx_comparisons", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### PolyPhen2 comparisons
###########################
stagenum <- 13
#All domains
doubledeepms_polyphen2_comparisons(
input_file = file.path(base_dir, paste0("009", "_doubledeepms_allostery_plots"), "dg_singles.txt"),
polyphen2_file = file.path(base_dir, "Data", "polyphen2", "poyphen2_short.txt"),
position_offset = list(
# "GB1" = 0,
"PSD95-PDZ3" = 0,
"GRB2-SH3" = 158),
uniprot_id = list(
# "GB1" = "",
"PSD95-PDZ3" = "DLG4_HUMAN",
"GRB2-SH3" = "GRB2_HUMAN"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_polyphen2_comparisons", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### 3did comparisons
###########################
stagenum <- 14
#All domains
doubledeepms_3did_comparisons(
input_file = file.path(base_dir, paste0("009", "_doubledeepms_allostery_plots"), "dg_singles.txt"),
threedid_file = file.path(base_dir, "Data", "3did", "3did_interface_flat"),
alignment_file_list = list(
"PSD95-PDZ3" = file.path(base_dir, "Data", "3did", "PSD95-PDZ3", "PF00595_seed_rat_human_align.fasta"),
"GRB2-SH3" = file.path(base_dir, "Data", "3did", "GRB2-SH3", "PF00018_seed_chicken_human_align.fasta")),
threedid_domain_name_list = list(
"PSD95-PDZ3" = "PDZ",
"GRB2-SH3" = "SH3_1"),
position_offset_list = list(
"PSD95-PDZ3" = 310,
"GRB2-SH3" = 0),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_3did_comparisons", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### EVE comparisons
###########################
stagenum <- 15
#All domains
doubledeepms_eve_comparisons(
eve_file_list = list(
"GB1" = file.path(base_dir, "Data", "EVE", "GB1", "SPG1_STRSG_218-292_11-26-2021_b05_single_mutant_matrix.csv"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "EVE", "PSD95-PDZ3", "DLG4_HUMAN_301-404_11-26-2021_b04_single_mutant_matrix.csv"),
"GRB2-SH3" = file.path(base_dir, "Data", "EVE", "GRB2-SH3", "GRB2_HUMAN_149-217_11-26-2021_b02_single_mutant_matrix.csv")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_eve_comparisons", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
}
lehner-lab/doubledeepms documentation built on July 21, 2023, 4:10 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions doubledeepms
Documented in doubledeepms
#' doubledeepms
#'
#' Main analysis script.
#'
#' @param startStage Start at a specified analysis stage (default:1)
#' @param stopStage Stop at a specified analysis stage (default:15)
#' @param base_dir Base directory for all output files (default:NB private CRG server path; change accordingly)
#' @param tmodel_job_number Thermodynamic model fit job number: 1:final model, 2-11: monte carlo simluations for confidence intervals of model-inferred free energies (default:1)
#' @param tmodel_grid_search Thermodynamic model fit grid search to determine optimal hyperparameters (default:FALSE)
#' @param tmodel_protein Thermodynamic model fit proteins: comma-separated list of names or 'all' (default:'GRB2-SH3')
#' @param tmodel_subset Thermodynamic model fit data subset: either an integer percentage of subsampled doubles (1-100) or "binding_only" or "singles_only" (default:100)
#'
#' @return Nothing
#' @export
doubledeepms <- function(
startStage = 1,
stopStage = 15,
base_dir = "/users/project/prj004631/afaure/DMS/Results/doubledeepms_proj",
tmodel_job_number = 1,
tmodel_grid_search = FALSE,
tmodel_protein = "GRB2-SH3",
tmodel_subset = 100
){
# startStage=1
# stopStage=15
# base_dir = "/users/project/prj004631/afaure/DMS/Results/doubledeepms_proj"
# rerun_raw = F
colour_scheme <- list(
"shade 0" = list(
"#F4270C",
"#F4AD0C",
"#1B38A6",
"#09B636"),
"shade 1" = list(
"#FFB0A5",
"#FFE4A5",
"#9DACE3",
"#97E9AD"),
"shade 2" = list(
"#FF6A56",
"#FFCB56",
"#4C63B7",
"#43C766"),
"shade 3" = list(
"#A31300",
"#A37200",
"#0C226F",
"#007A20"),
"shade 4" = list(
"#410800",
"#412D00",
"#020B2C",
"#00300D"),
"shade 5" = list(
"#CCCCCC",
"#FF991F",
"#5CB8FF",
"#B22222"
))
#First and last analysis stages
first_stage <- startStage
last_stage <- stopStage
### Fit thermo models
###########################
stagenum <- 0
doubledeepms_fit_thermo_model(
base_dir = base_dir,
tmodel_job_number = tmodel_job_number,
tmodel_grid_search = tmodel_grid_search,
tmodel_protein = tmodel_protein,
tmodel_subset = as.character(tmodel_subset),
tmodel_hyperparameters = file.path(base_dir, "Data", "mochi", "hyperparameters.txt"),
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Evaluate thermo model results
###########################
stagenum <- 1
#GB1
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 2%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample2p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample2p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 5%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample5p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample5p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 10%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample10p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample10p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 20%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample20p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample20p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GB1 - subsample doubles 50%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample50p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GB1_literature_free_energies.txt"),
position_offset = 1,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GB1subsample50p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - binding only
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_bindingonly"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3bindingonly", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - singles only
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_singlesonly"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3singlesonly", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 2%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample2p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample2p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 5%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample5p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample5p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 10%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample10p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample10p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 20%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample20p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample20p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3 - subsample doubles 50%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample50p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "PDZ_literature_free_energies.txt"),
position_offset = 310,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_PSD95-PDZ3subsample50p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - binding only
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_bindingonly"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3bindingonly", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - singles only
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_singlesonly"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3singlesonly", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 2%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample2p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample2p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 5%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample5p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample5p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 10%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample10p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample10p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 20%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample20p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample20p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3 - subsample doubles 50%
doubledeepms_thermo_model_results(
mochi_outpath = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample50p"),
literature_free_energies = file.path(base_dir, "Data", "in_vitro", "GRB2_literature_free_energies.txt"),
position_offset = 0,
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_thermo_model_results_GRB2-SH3subsample50p", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Add 3D structure metrics
###########################
stagenum <- 2
#GB1
doubledeepms_structure_metrics(
input_file = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_GB1"), "dg_singles.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_structure_metrics_GB1", stagenum=stagenum, base_dir=base_dir),
pdb_file = file.path(base_dir, "Data", "pdb", "1fcc.pdb"),
pdb_chain_query = "C",
pdb_chain_target = "A",
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_structure_metrics(
input_file = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_PSD95-PDZ3"), "dg_singles.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_structure_metrics_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
pdb_file = file.path(base_dir, "Data", "pdb", "1be9.pdb"),
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_structure_metrics(
input_file = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_GRB2-SH3"), "dg_singles.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_structure_metrics_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
pdb_file = file.path(base_dir, "Data", "pdb", "2vwf.pdb"),
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Fitness plots
###########################
stagenum <- 3
#PSD95-PDZ3 and GRB2-SH3
doubledeepms_fitness_plots(
fitness_list = list(
"GB1" = file.path(base_dir, "Data", "fitness", "GB1"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "fitness", "PSD95-PDZ3"),
"GRB2-SH3" = file.path(base_dir, "Data", "fitness", "GRB2-SH3")),
structure_metrics_list = list(
"GB1" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
"PSD95-PDZ3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
"GRB2-SH3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt")),
val_inpath = file.path(base_dir, "Data", "experimental_validations", "GRB2-SH3", "experimenal_validations_ODs.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_fitness_plots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Plot fitness heatmaps
###########################
stagenum <- 4
#GB1
doubledeepms_fitness_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
input_file_fitness = file.path(base_dir, "Data", "fitness", "GB1"),
domain_name = "GB1",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_fitness_heatmaps_GB1", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 11,
plot_traits = "Binding",
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_fitness_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
input_file_fitness = file.path(base_dir, "Data", "fitness", "PSD95-PDZ3"),
input_file_MSA = file.path(base_dir, "Data", "MSA", "PSD95-PDZ3", "frequencies.csv"),
domain_name = "PSD95 PDZ3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_fitness_heatmaps_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 15,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_fitness_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt"),
input_file_fitness = file.path(base_dir, "Data", "fitness", "GRB2-SH3"),
input_file_MSA = file.path(base_dir, "Data", "MSA", "GRB2-SH3", "frequencies.csv"),
domain_name = "GRB2 SH3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_fitness_heatmaps_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 11,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Plot free energy scatterplots
###########################
stagenum <- 5
#All domains
doubledeepms_free_energy_scatterplots(
input_list = list(
"GB1" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
"PSD95-PDZ3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
"GRB2-SH3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt")),
input_MSA_list = list(
"GB1" = file.path(base_dir, "Data", "MSA", "GB1", "frequencies.csv"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "MSA", "PSD95-PDZ3", "frequencies.csv"),
"GRB2-SH3" = file.path(base_dir, "Data", "MSA", "GRB2-SH3", "frequencies.csv")
),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_free_energy_scatterplots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Plot free energy heatmaps
###########################
stagenum <- 6
#GB1
doubledeepms_free_energy_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
domain_name = "GB1",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_free_energy_heatmaps_GB1", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 11,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_free_energy_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
domain_name = "PSD95 PDZ3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_free_energy_heatmaps_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 15,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_free_energy_heatmaps(
input_file = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt"),
domain_name = "GRB2 SH3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_free_energy_heatmaps_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
plot_width = 11,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Protein stability plots
###########################
stagenum <- 7
#All domains
doubledeepms_protein_stability_plots(
input_list = list(
"GB1" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
"PSD95-PDZ3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
"GRB2-SH3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt")),
pdb_file_list = list(
"GB1" = file.path(base_dir, "Data", "pdb", "1fcc.pdb"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "pdb", "1be9.pdb"),
"GRB2-SH3" = file.path(base_dir, "Data", "pdb", "2vwf.pdb")),
pdb_chain_query_list = list(
"GB1" = "C",
"PSD95-PDZ3" = "A",
"GRB2-SH3" = "A"),
aaprop_file = file.path(base_dir, "Data", "amino_acid_properties", "amino_acid_properties_annotated_supplementary.txt"),
aaprop_file_selected = file.path(base_dir, "Data", "amino_acid_properties", "selected.amino_acid_properties.txt"),
input_MSA_list = list(
"GB1" = file.path(base_dir, "Data", "MSA", "GB1", "frequencies.csv"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "MSA", "PSD95-PDZ3", "frequencies.csv"),
"GRB2-SH3" = file.path(base_dir, "Data", "MSA", "GRB2-SH3", "frequencies.csv")
),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_protein_stability_plots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Binding interface plots
###########################
stagenum <- 8
# GRB2-SH3
doubledeepms_interface_mechanisms(
base_dir = base_dir,
domain_name = "GRB2-SH3",
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_ligand_interface_plots", stagenum=stagenum, base_dir=base_dir),
mut_subset_list = list(
c("T", "F","Q","H", "S", "V", "I", "C"),
c("T", "S", "L", "V", "A", "K", "R")),
pos_subset_list = list(
c(7, 51),
c(46)),
ligand_pos_list = list(
c(3,4),
c(11)),
pdb_id = "2vwf",
pdb_view = "(0.837024331,0.261427671,0.480670929,0.209657252,0.658192515,-0.723066926,-0.505404055,0.706001341,0.496113181,0.000000000,0.000000000,-141.782043457,-2.309909821,13.775757790,0.139801025,111.782043457,171.782043457,-20.000000000 )",
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
# All domains
doubledeepms_binding_interface(
input_list = list(
"GB1" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GB1"), "dg_singles.txt"),
"PSD95-PDZ3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_PSD95-PDZ3"), "dg_singles.txt"),
"GRB2-SH3" = file.path(base_dir, paste0("002", "_doubledeepms_structure_metrics_GRB2-SH3"), "dg_singles.txt")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_binding_interface", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Allostery plots
###########################
stagenum <- 9
#All domains
doubledeepms_allostery_plots(
input_file = file.path(base_dir, paste0("007", "_doubledeepms_protein_stability_plots"), "dg_singles.txt"),
pdb_file_list = list(
"GB1" = file.path(base_dir, "Data", "pdb", "1fcc.pdb"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "pdb", "1be9.pdb"),
"GRB2-SH3" = file.path(base_dir, "Data", "pdb", "2vwf.pdb")),
pdb_chain_query_list = list(
"GB1" = "C",
"PSD95-PDZ3" = "A",
"GRB2-SH3" = "A"),
annotation_list = list(
"PSD95-PDZ3" = file.path(base_dir, "Data", "annotations", "PSD95-PDZ3", "PSD95-PDZ3_annotations.txt")),
ohm_file_list = list(
"GB1" = file.path(base_dir, "Data", "ohm", "ohm_2gb1_ddPCA_GB1only.txt"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "ohm", "ohm_1be9_ddPCA_PDZonly.txt"),
"GRB2-SH3" = file.path(base_dir, "Data", "ohm", "ohm_2vwf_ddPCA_GRB2only.txt")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_allostery_plots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Allostery scatterplots
###########################
stagenum <- 10
#All domains
doubledeepms_allostery_scatterplots(
input_file = file.path(base_dir, paste0("009", "_doubledeepms_allostery_plots"), "dg_singles.txt"),
fitness_list = list(
"PSD95-PDZ3" = file.path(base_dir, "Data", "fitness", "PSD95-PDZ3"),
"GRB2-SH3" = file.path(base_dir, "Data", "fitness", "GRB2-SH3")),
mochi_outpath_list = list(
"PSD95-PDZ3" = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128"),
"GRB2-SH3" = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_allostery_scatterplots", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Downsampling analysis
###########################
stagenum <- 11
#GB1
doubledeepms_downsampling_analysis(
mochi_outpath_prefix = file.path(base_dir, "Data", "mochi", "GB1", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample"),
sample_percentage = c(2, 5, 10, 20, 50, 100),
literature_comparison_prefix = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_GB1subsample")),
literature_comparison_list = list(
"folding" = "validation_scatter_(mAvg)_mean_f_ddg_conf.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_downsampling_analysis_GB1", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#GRB2-SH3
doubledeepms_downsampling_analysis(
mochi_outpath_prefix = file.path(base_dir, "Data", "mochi", "GRB2-SH3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample"),
sample_percentage = c(2, 5, 10, 20, 50, 100),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_downsampling_analysis_GRB2-SH3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
#PSD95-PDZ3
doubledeepms_downsampling_analysis(
mochi_outpath_prefix = file.path(base_dir, "Data", "mochi", "PSD95-PDZ3", "mochi__fit_tmodel_3state_sparse_dimsum128_subsample"),
sample_percentage = c(2, 5, 10, 20, 50, 100),
literature_comparison_prefix = file.path(base_dir, paste0("001", "_doubledeepms_thermo_model_results_PSD95-PDZ3subsample")),
literature_comparison_list = list(
"folding" = "validation_scatter_Calosci_2008_f_ddg_conf.txt",
"binding" = "validation_scatter_Laursen_2020_b_ddg_conf.txt"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_downsampling_analysis_PSD95-PDZ3", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### Foldx comparisons
###########################
stagenum <- 12
#All domains
doubledeepms_foldx_comparisons(
input_file = file.path(base_dir, paste0("009", "_doubledeepms_allostery_plots"), "dg_singles.txt"),
foldx_file_list = list(
"GB1" = file.path(base_dir, "Data", "foldx", "GB1", "PS_2gb1_nowater_noligand_restrict_scanning_output.txt"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "foldx", "PSD95-PDZ3", "PS_1be9_nowater_noligand_restrict_scanning_output.txt"),
"GRB2-SH3" = file.path(base_dir, "Data", "foldx", "GRB2-SH3", "PS_2vwf_nowater_noligand_restrict_scanning_output.txt")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_foldx_comparisons", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### PolyPhen2 comparisons
###########################
stagenum <- 13
#All domains
doubledeepms_polyphen2_comparisons(
input_file = file.path(base_dir, paste0("009", "_doubledeepms_allostery_plots"), "dg_singles.txt"),
polyphen2_file = file.path(base_dir, "Data", "polyphen2", "poyphen2_short.txt"),
position_offset = list(
# "GB1" = 0,
"PSD95-PDZ3" = 0,
"GRB2-SH3" = 158),
uniprot_id = list(
# "GB1" = "",
"PSD95-PDZ3" = "DLG4_HUMAN",
"GRB2-SH3" = "GRB2_HUMAN"),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_polyphen2_comparisons", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### 3did comparisons
###########################
stagenum <- 14
#All domains
doubledeepms_3did_comparisons(
input_file = file.path(base_dir, paste0("009", "_doubledeepms_allostery_plots"), "dg_singles.txt"),
threedid_file = file.path(base_dir, "Data", "3did", "3did_interface_flat"),
alignment_file_list = list(
"PSD95-PDZ3" = file.path(base_dir, "Data", "3did", "PSD95-PDZ3", "PF00595_seed_rat_human_align.fasta"),
"GRB2-SH3" = file.path(base_dir, "Data", "3did", "GRB2-SH3", "PF00018_seed_chicken_human_align.fasta")),
threedid_domain_name_list = list(
"PSD95-PDZ3" = "PDZ",
"GRB2-SH3" = "SH3_1"),
position_offset_list = list(
"PSD95-PDZ3" = 310,
"GRB2-SH3" = 0),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_3did_comparisons", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
### EVE comparisons
###########################
stagenum <- 15
#All domains
doubledeepms_eve_comparisons(
eve_file_list = list(
"GB1" = file.path(base_dir, "Data", "EVE", "GB1", "SPG1_STRSG_218-292_11-26-2021_b05_single_mutant_matrix.csv"),
"PSD95-PDZ3" = file.path(base_dir, "Data", "EVE", "PSD95-PDZ3", "DLG4_HUMAN_301-404_11-26-2021_b04_single_mutant_matrix.csv"),
"GRB2-SH3" = file.path(base_dir, "Data", "EVE", "GRB2-SH3", "GRB2_HUMAN_149-217_11-26-2021_b02_single_mutant_matrix.csv")),
outpath = doubledeepms__format_dir(dir_suffix="_doubledeepms_eve_comparisons", stagenum=stagenum, base_dir=base_dir),
colour_scheme = colour_scheme,
execute = (first_stage <= stagenum & last_stage >= stagenum))
}
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