Tumour Evolution Simulation
  1. Tumour Evolution Simulation

simulation-devel

Public
  1. Tumour Evolution Simulation
  2. simulation-devel

Commits

AuthorCommitMessageCommit dateIssues
Yoshua WakehamYoshua Wakeham
ee686925109Implement __repr__ for remaining classes, and revamp subpop.info() method
Yoshua WakehamYoshua Wakeham
a18c27b8c49Make Treatment an abstract base class, and create concrete SingleDoseTreatment class
Yoshua WakehamYoshua Wakeham
d06b3d7dcc5Ensure population archive is extracted to run dir, to avoid simulations overwriting each other
Yoshua WakehamYoshua Wakeham
7bd6937e12dTweaks to loading procedure, including timing the load, and trying to resolve select_time inconsistency
Yoshua WakehamYoshua Wakeham
5b7e27f7a36Fix bug with required, mutually-exclusive cmd line params
Yoshua WakehamYoshua Wakeham
5a7565f39eaUpdate default config file and run_param_set to include loading option
Yoshua WakehamYoshua Wakeham
008ee2774ebLet store_flag_and_vars take multiple variables
Yoshua WakehamYoshua Wakeham
e049c4e8c0fCondense initial diversity cmd line params
Yoshua WakehamYoshua Wakeham
efaa4b1ae47Add cmd line param to allow snapshot loading
Yoshua WakehamYoshua Wakeham
2eb86bbd57bImplement popn loading procedure in Simulator
Yoshua WakehamYoshua Wakeham
8b0e40c5ab8Add start_cycle parameter to simulator.run()
Yoshua WakehamYoshua Wakeham
c5bba1eb1adStore analytics in snapshot
Yoshua WakehamYoshua Wakeham
28012d9d25bAdd t_curr to saved parameters
Yoshua WakehamYoshua Wakeham
6fb1d59fbe4Remove seemingly unused treatment params from simulator object
Yoshua WakehamYoshua Wakeham
9196a01c2cbIgnore undo files
Yoshua WakehamYoshua Wakeham
d36a96ef0e2Remove unused simulator.is_running flag
Yoshua WakehamYoshua Wakeham
18e5f4d697dImplement neutral mutation count; remove neutral mutations from clone mut dictionaries
Yoshua WakehamYoshua Wakeham
f91d99a775fAdd classify_neutral method to Mutation class
Yoshua WakehamYoshua Wakeham
ebc9f4d809cAdd creation timestamp to Mutation class
Yoshua WakehamYoshua Wakeham
4ee0b827007Change default size limit to 10million
Yoshua WakehamYoshua Wakeham
68e8ebc0d42Add __repr__ methods for simulator, analytics
Yoshua WakehamYoshua Wakeham
4d06468430eAdd manual garbage collection after pruning dead-end clones, in case this improves mem usage
Yoshua WakehamYoshua Wakeham
32f89d434ecFix error in cmd line param names
Yoshua WakehamYoshua Wakeham
8407c5d7267Add cmd line param for saving snapshot
Yoshua WakehamYoshua Wakeham
ed4ca868383Organise cmd line params
Yoshua WakehamYoshua Wakeham
3056d510002Clean up and simplify snapshot.py
Yoshua WakehamYoshua Wakeham
5559805e23bMove all constants to new constants module
Yoshua WakehamYoshua Wakeham
f118106df65Move beta dist sample from global (simulator) attribute, to method in mutation module
Yoshua WakehamYoshua Wakeham
1556b301d0cClean up files after loading population from archive
Yoshua WakehamYoshua Wakeham
cbc75af9d97Remove get_beta_dist_sample from pickled opt, and use repr() for writing the CSV files
Yoshua WakehamYoshua Wakeham
537688d57f8Fix bug in Population.init_from_file
Yoshua WakehamYoshua Wakeham
a50e7622554Add filepath argument to save_population func
Yoshua WakehamYoshua Wakeham
e6669cce115Implement init_from_file func for Population
Yoshua WakehamYoshua Wakeham
f6e8f489f96Implement param storage, and rewrite main save/load funcs to take/return population objects
Yoshua WakehamYoshua Wakeham
52777a04b7fCreate file with functions for saving/loading populations to file.Still work in progress.
Yoshua WakehamYoshua Wakeham
9eb7590193dCreate class method to load mutation from file
Yoshua WakehamYoshua Wakeham
2fe452c6120Create class method to load subpop from file; also add object counter for generating clone IDs
Yoshua WakehamYoshua Wakeham
f73c5b27f0cVarious changes to clone plot
Yoshua WakehamYoshua Wakeham
22386ceec8aTweak legend location on clone plot
Yoshua WakehamYoshua Wakeham
4e7001fe4c9Allow asymmetric neutral thresholds for pos/neg mutations.Set neg to 1%, pos to 5%.
Yoshua WakehamYoshua Wakeham
3fecbb31b25Prune dead mutations before generating resistance
Yoshua WakehamYoshua Wakeham
7c968cb941cRename is_dead_end to is_dead_leaf, and add new is_dead_end func
Yoshua WakehamYoshua Wakeham
6109e3bc811Squash bug in switch_mutn_type causing sims to crash
Yoshua WakehamYoshua Wakeham
6031f4812fcAdd switch_mutn_type() mutator func to fix errors where mut_type was changed but mutn wasn't moved to correct list in all_muts
Yoshua WakehamYoshua Wakeham
45602a5ebb1Write extra clone summary just after resistance is generated
Yoshua WakehamYoshua Wakeham
e3c0083bf5cSimplify make_plot and make_dual_plot functions
Yoshua WakehamYoshua Wakeham
022c1b8b023Working on simplifying plotting functions.WORK IN PROGRESS, currently broken
Yoshua WakehamYoshua Wakeham
b74e99f40f6Change scale of clone size plot to symlog (linear near 0, log elsewhere)
Yoshua WakehamYoshua Wakeham
958cda68a60Add matplotlibrc for global default plot settings
Yoshua WakehamYoshua Wakeham
00cac76de31Keep working on clonal frequency plot