e1b8e103ea
saving from my panino, made lineage dist plots
2022-08-04 13:47:24 +01:00
1efb534f0f
fix some derps
2022-08-04 13:46:52 +01:00
61c7a30835
minor tidy and leble adjust sizes for simple barplots
2022-08-04 10:26:18 +01:00
bcba0c359e
moved code for structure figure to sep sir
2022-08-03 21:33:19 +01:00
aabe466599
added plots for thesis
2022-08-03 21:32:55 +01:00
41c4996426
more of the previous thing
2022-08-03 20:51:32 +01:00
bdbc97c40a
fix many plot functions to stop them using the "g=ggplot()" pattern,
...
which annoyingly throws away lots of useful data that RShiny needs for
clickable plots. Also split the "flame bar" for ligand distance out into
separate functions in generate_distance_colour_map.R. This can now be
easily incorporated into any "wide" graph showing all positions.
2022-08-03 18:58:27 +01:00
e498d46f8b
consurf plot: add debug option. logoP SNP: distance flame tiles
2022-08-03 18:58:27 +01:00
f2709f3992
added replace b factor scripts for lig affinity and ppi2
2022-08-02 20:30:43 +01:00
87a3d7acf2
generated simple affinity plots for embb
2022-08-02 20:29:31 +01:00
214e9232c6
still trying affinity phew
2022-08-02 16:55:31 +01:00
d94aa10c9b
saving work
2022-08-01 21:44:11 +01:00
66337c289c
added scripts to generate mean stability for rpob
2022-08-01 21:41:55 +01:00
ccc877e811
attempting affintiy stuff
2022-08-01 21:41:02 +01:00
0d8979dfcb
separted cols
2022-08-01 14:09:46 +01:00
e750ee59aa
saving
2022-08-01 13:41:43 +01:00
79c261963b
sorting the ensemble and priority for ligand affinity
2022-08-01 13:36:05 +01:00
f3710bfaf5
added mcsm_mean_affinity_ensemble.R and replaceBfactor_pdb_stability.R
2022-07-31 19:25:28 +01:00
1bf66b145c
separating mcsm_mean_stability_ensemble from combined script
2022-07-31 19:24:35 +01:00
06e5363112
added scriptaa mcsm_mean_stability_ensemble.R to get ensemble of averages across predictors for stability and affinity
2022-07-31 16:29:47 +01:00
4de1e800ec
moved mut_landscape files to plotting
2022-07-31 12:01:56 +01:00
d6a63eed21
added mut_landscape.R that outputs the mutational positions and annotations for generating the structural landscape of all gene-targets
2022-07-31 12:01:56 +01:00
26f284d76e
added test_func_combined.py
2022-07-29 00:14:39 +01:00
9cd6613da6
added cm_logo_skf_v2.py
2022-07-29 00:13:54 +01:00
e55906d2c7
saving work
2022-07-29 00:12:43 +01:00
1695e90b42
running none_complete with diff cv threhsolds
2022-07-28 15:33:43 +01:00
85f59155fa
uncommented all models for a full run
2022-07-28 15:28:31 +01:00
37f5199c5c
added the cm_ml_iterator_TODO.py for later
2022-07-28 15:25:31 +01:00
e32308d984
moved old logs
2022-07-28 15:24:49 +01:00
fd0ccc9032
added genes_ml_logs
2022-07-28 15:23:49 +01:00
cd68e60f09
updated running_scripts with added rt and none and none_bts
2022-07-28 15:22:44 +01:00
d3d5698a3e
added MultClfs_CVs.py and ml_iterator_CVs.py
2022-07-28 15:19:58 +01:00
b87f8d0295
trying diff cv thresholds for single gene
2022-07-28 15:19:13 +01:00
8d8a61675f
various edits
2022-07-28 13:20:14 +01:00
90b9477520
ml_iterator tweaks
2022-07-28 13:19:58 +01:00
584b866f0b
moved ../ml_functions/MultClfs_logo_skf.py to del
2022-07-28 12:25:29 +01:00
2c50124b1b
moved logo_skf function to del as using the MultClfs for combined data
2022-07-28 12:24:24 +01:00
a6532ddfa3
just running for pnca
2022-07-27 17:11:30 +01:00
744bc8f4a1
added dummy classifier to models
2022-07-27 17:10:04 +01:00
c32005c99c
adding other split types on ml_iterator
2022-07-27 15:58:15 +01:00
63c8876764
checking the splitTTS script to make sure other splits have been factored in
2022-07-27 15:52:20 +01:00
f4cab1fdfb
fixed masking condition for ML training data for genes and wrote revised mask files out
2022-07-27 13:36:16 +01:00
0adf69f75a
added model names sklearn
2022-07-16 15:35:42 +01:00
39e72b2dfb
added all_estimators
2022-07-16 13:32:19 +01:00
a590354f15
saving work from panino
2022-07-12 10:14:06 +01:00
33e3b5a0a6
various bugs
2022-07-12 10:14:06 +01:00
6950c4b057
added reverse traininig as split type in SplitTTS.py
2022-07-11 20:03:06 +01:00
1965517681
added other split_type options i.e none and none with bts
2022-07-11 19:27:14 +01:00
ce730fbe57
uncommented
2022-07-10 13:29:01 +01:00
350be30f19
minor changes to run combined_model
2022-07-10 13:23:13 +01:00
