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b8653c6afe
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ML scripts: {'n_jobs': os.cpu_count() }
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2022-07-02 10:22:07 +01:00 |
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cbfa9ff31b
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lineage plots: be a function and then run over all pairs
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2022-06-29 19:24:47 +01:00 |
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8965bee5d6
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LINEAGE2 plots: p value stars
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2022-06-29 17:18:55 +01:00 |
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c85c965c3e
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added TODO for lineage2.R
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2022-06-29 10:26:08 +01:00 |
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aff7247e3b
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really!?!?!?!?
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2022-06-28 21:52:04 +01:00 |
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478df927cc
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horrible lineage analysis hell
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2022-06-28 21:51:02 +01:00 |
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f355846dae
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added active site indication for merged_dfs in count_vars_ML.R and also added 'gene_name' in combining_dfs.py
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2022-06-15 18:36:28 +01:00 |
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2274f01f23
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combined msa and wt seq into 1 list so only list is passed as an arg for plotting ED plots
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2022-02-15 08:31:58 +00:00 |
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18e1f14455
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saving changes
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2022-02-14 11:14:40 +00:00 |
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6ffb084546
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added hbond residues in config for all genes
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2022-02-09 15:59:18 +00:00 |
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7a14655ecb
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added active site positions to all config.R
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2022-02-03 18:02:27 +00:00 |
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04cddbbf2b
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minor formatting, taken a line off the barplots_subcolours_aa_PS.R
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2022-02-02 19:01:13 +00:00 |
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3e5191f5c6
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attempting to visualise consurf plot along with highlighting active site pos
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2022-02-02 19:00:23 +00:00 |
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9c3818fd98
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added NOTE to the barplots_subcolours_aa_PS.R as I am trying it for other plots
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2022-02-02 18:59:33 +00:00 |
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3d45780c1a
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updated docs for dm_om_data.R
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2022-02-01 16:23:03 +00:00 |
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e795c00831
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added gene conditions to test_dm_om_data.R
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2022-02-01 10:54:10 +00:00 |
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b2e035d9bc
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moved old dm_om_data_nf to redundant/
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2022-01-31 17:52:29 +00:00 |
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ef1fb96b88
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tested dm_om_data function with alr gene to make sure valid dfs are being returned
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2022-01-31 17:50:12 +00:00 |
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a287b801f7
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saving before commiting
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2022-01-31 17:36:00 +00:00 |
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cd772e9df1
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moved corr_data.R to redundant/
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2022-01-29 17:34:18 +00:00 |
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a4a4890634
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added FIXME to fix dm_om data for targets other than gid
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2022-01-29 17:30:19 +00:00 |
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5346431256
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repurposing corr_data.R into a function to allow required params to be passed in
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2022-01-29 17:24:15 +00:00 |
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5f9a95ccb1
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moved Header_TT.R from plotting/ to scripts
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2022-01-26 11:54:38 +00:00 |
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dec6c72fb5
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more header_tt
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2022-01-26 11:50:50 +00:00 |
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586927ca56
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wholesale change for Header_TT.R location
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2022-01-26 11:39:03 +00:00 |
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b133b8be24
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save content
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2022-01-26 11:34:59 +00:00 |
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3bc5dcbad3
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renamed logoP_msa.R --> logoP_msa_raw.R
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2022-01-26 11:03:45 +00:00 |
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6a9f4a0cab
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added logoP_logolas.R to plot logolas like plot to show ED regions
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2022-01-24 17:23:32 +00:00 |
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b72ffb5d2c
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just tested logo plot msa with embb after correcting the OMINOUS fasta file
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2022-01-19 18:57:04 +00:00 |
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e2cdee2d08
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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
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2022-01-18 17:36:54 +00:00 |
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8f8a9db92c
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tried ED logo, but needs work
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2022-01-18 16:53:16 +00:00 |
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00094f036a
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playing with MSA plots to allow filtering of positions, arghhh
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2022-01-18 15:30:41 +00:00 |
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9546355241
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updated and tested logoP_snp.R. All done nicely
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2022-01-15 13:17:26 +00:00 |
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3b7cea3c47
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adding legend forlogo plot
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2022-01-14 10:18:01 +00:00 |
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344a74a9e1
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saving work for logo plots
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2022-01-13 18:53:47 +00:00 |
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3f7bc908ec
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going through functions and script for interactive plots
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2022-01-12 17:58:16 +00:00 |
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1f266c4cb8
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more tidying and formatting for combining_dfs.py. Hopefully no more after today
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2022-01-11 17:51:28 +00:00 |
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c48fa1dbb0
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minor tidy up to check interactive graphs Rshiny
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2022-01-07 16:07:44 +00:00 |
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b66cf31219
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added untracked files in scripts/plotting
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2022-01-04 12:27:25 +00:00 |
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00b84ccb1c
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handled rpob 5uhc position offset in mcsm_ppi2
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2022-01-04 10:45:29 +00:00 |
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c32de1bf0f
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Merge branch 'embb_dev'
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2021-11-12 14:37:10 +00:00 |
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dad8f526a2
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added TESTING_plots.R
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2021-11-09 13:55:21 +00:00 |
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746889b075
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saving work for the day after massive repurpose
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2021-09-15 19:48:56 +01:00 |
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1d16c6848e
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moved coloured_bp_data.R to redundant in light of updated function and reflected this in notes withing get_plotting_dfs.R
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2021-09-15 19:42:08 +01:00 |
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7550efbd4c
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added wideplot subcols generation within bp_subcolours.R to make it easier to call the whole thing as a function and use merged_df3 to generate plot without having to separately generate special data for it. Tested with real data on different stability params
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2021-09-15 19:29:09 +01:00 |
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449af7acf4
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fixed pos_count cals in function by specifying dplyr and changed summarize to summarise
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2021-09-15 15:46:42 +01:00 |
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996d67b423
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added pretty colnames to corr_data.R
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2021-09-13 10:24:41 +01:00 |
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3f3fe89a6b
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added shorter scripts for each different processing for plots to make it wasire to read code
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2021-09-10 18:20:45 +01:00 |
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5c8a9e8f00
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sorted combining_dfs.py with all other data files and tidied up get_plotting_dfs.R
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2021-09-10 18:16:41 +01:00 |
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4ba4ff602e
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added foldx_scaled and deepddg_scaled values added to combine_df.py and also used that script to merge all the dfs so that merged_df2 and merged_df3 are infact what we need for downstream processing
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2021-09-10 16:58:36 +01:00 |
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