Commit graph

240 commits

Author SHA1 Message Date
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
8079dd7b6c reran to generate merged_df3 with correct dst for dst muts. modified combining_dfs_plotting.R 2022-07-08 21:33:57 +01:00
b8653c6afe ML scripts: {'n_jobs': os.cpu_count() } 2022-07-02 10:22:07 +01:00
cbfa9ff31b lineage plots: be a function and then run over all pairs 2022-06-29 19:24:47 +01:00
8965bee5d6 LINEAGE2 plots: p value stars 2022-06-29 17:18:55 +01:00
c85c965c3e added TODO for lineage2.R 2022-06-29 10:26:08 +01:00
aff7247e3b really!?!?!?!? 2022-06-28 21:52:04 +01:00
478df927cc horrible lineage analysis hell 2022-06-28 21:51:02 +01:00
f355846dae added active site indication for merged_dfs in count_vars_ML.R and also added 'gene_name' in combining_dfs.py 2022-06-15 18:36:28 +01:00
2274f01f23 combined msa and wt seq into 1 list so only list is passed as an arg for plotting ED plots 2022-02-15 08:31:58 +00:00
18e1f14455 saving changes 2022-02-14 11:14:40 +00:00
6ffb084546 added hbond residues in config for all genes 2022-02-09 15:59:18 +00:00
7a14655ecb added active site positions to all config.R 2022-02-03 18:02:27 +00:00
04cddbbf2b minor formatting, taken a line off the barplots_subcolours_aa_PS.R 2022-02-02 19:01:13 +00:00
3e5191f5c6 attempting to visualise consurf plot along with highlighting active site pos 2022-02-02 19:00:23 +00:00
9c3818fd98 added NOTE to the barplots_subcolours_aa_PS.R as I am trying it for other plots 2022-02-02 18:59:33 +00:00
3d45780c1a updated docs for dm_om_data.R 2022-02-01 16:23:03 +00:00
e795c00831 added gene conditions to test_dm_om_data.R 2022-02-01 10:54:10 +00:00
b2e035d9bc moved old dm_om_data_nf to redundant/ 2022-01-31 17:52:29 +00:00
ef1fb96b88 tested dm_om_data function with alr gene to make sure valid dfs are being returned 2022-01-31 17:50:12 +00:00
a287b801f7 saving before commiting 2022-01-31 17:36:00 +00:00
cd772e9df1 moved corr_data.R to redundant/ 2022-01-29 17:34:18 +00:00
a4a4890634 added FIXME to fix dm_om data for targets other than gid 2022-01-29 17:30:19 +00:00
5346431256 repurposing corr_data.R into a function to allow required params to be passed in 2022-01-29 17:24:15 +00:00
5f9a95ccb1 moved Header_TT.R from plotting/ to scripts 2022-01-26 11:54:38 +00:00
dec6c72fb5 more header_tt 2022-01-26 11:50:50 +00:00
586927ca56 wholesale change for Header_TT.R location 2022-01-26 11:39:03 +00:00
b133b8be24 save content 2022-01-26 11:34:59 +00:00
3bc5dcbad3 renamed logoP_msa.R --> logoP_msa_raw.R 2022-01-26 11:03:45 +00:00
6a9f4a0cab added logoP_logolas.R to plot logolas like plot to show ED regions 2022-01-24 17:23:32 +00:00
b72ffb5d2c just tested logo plot msa with embb after correcting the OMINOUS fasta file 2022-01-19 18:57:04 +00:00
e2cdee2d08 added additional check in combining_df_plotting.R to account for check when generating merged_df2 as muts NOT present in mcsm can create trouble, so fixed that and ran it successfully for alr and katg 2022-01-18 17:36:54 +00:00
8f8a9db92c tried ED logo, but needs work 2022-01-18 16:53:16 +00:00
00094f036a playing with MSA plots to allow filtering of positions, arghhh 2022-01-18 15:30:41 +00:00
9546355241 updated and tested logoP_snp.R. All done nicely 2022-01-15 13:17:26 +00:00
3b7cea3c47 adding legend forlogo plot 2022-01-14 10:18:01 +00:00
344a74a9e1 saving work for logo plots 2022-01-13 18:53:47 +00:00
3f7bc908ec going through functions and script for interactive plots 2022-01-12 17:58:16 +00:00
1f266c4cb8 more tidying and formatting for combining_dfs.py. Hopefully no more after today 2022-01-11 17:51:28 +00:00
c48fa1dbb0 minor tidy up to check interactive graphs Rshiny 2022-01-07 16:07:44 +00:00
b66cf31219 added untracked files in scripts/plotting 2022-01-04 12:27:25 +00:00
00b84ccb1c handled rpob 5uhc position offset in mcsm_ppi2 2022-01-04 10:45:29 +00:00
c32de1bf0f Merge branch 'embb_dev' 2021-11-12 14:37:10 +00:00
dad8f526a2 added TESTING_plots.R 2021-11-09 13:55:21 +00:00
746889b075 saving work for the day after massive repurpose 2021-09-15 19:48:56 +01:00