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gidb_dev

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• 1c1e98ad4f added get_logo_heights() in my_logolas.R Tanushree Tunstall 2022-01-26 11:16:02 +00:00
• 92af9fd565 combined logolas and raw data msa plots into 1 script and called it the same as before logoP_msa.R Tanushree Tunstall 2022-01-26 11:06:04 +00:00
• 6365fff858 moved logoP_msa_raw to redundant Tanushree Tunstall 2022-01-26 11:04:21 +00:00
• 3bc5dcbad3 renamed logoP_msa.R --> logoP_msa_raw.R Tanushree Tunstall 2022-01-26 11:03:45 +00:00
• 6a9f4a0cab added logoP_logolas.R to plot logolas like plot to show ED regions Tanushree Tunstall 2022-01-24 17:23:32 +00:00
• 9aa62b33b1 added my_logolas.R Tanushree Tunstall 2022-01-24 13:46:50 +00:00
• febb8f0f7f checked embb logo msa plot with chosen positions Tanushree Tunstall 2022-01-19 19:04:43 +00:00
• b72ffb5d2c just tested logo plot msa with embb after correcting the OMINOUS fasta file Tanushree Tunstall 2022-01-19 18:57:04 +00:00
• 59eaf58747 now definitely checked for all targets Tanushree Tunstall 2022-01-18 17:43:21 +00:00
• b9d173a2c4 checked combining_dfs.R for all targets Tanushree Tunstall 2022-01-18 17:42:04 +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 Tanushree Tunstall 2022-01-18 17:36:54 +00:00
• 8f8a9db92c tried ED logo, but needs work Tanushree Tunstall 2022-01-18 16:53:16 +00:00
• 00094f036a playing with MSA plots to allow filtering of positions, arghhh Tanushree Tunstall 2022-01-18 15:30:41 +00:00
• 08bd8a2ee5 added config files for R plots Tanushree Tunstall 2022-01-18 11:15:03 +00:00
• 4e779b2945 saving work Tanushree Tunstall 2022-01-18 11:14:25 +00:00
• ef4ac81a8a added config file for alr Tanushree Tunstall 2022-01-17 19:12:15 +00:00
• c8c4afb28a added logoP_msa.R Tanushree Tunstall 2022-01-17 19:11:48 +00:00
• 68a092037b finding seq discrepancy in MSA for embb Tanushree Tunstall 2022-01-17 19:11:10 +00:00
• af04c69d66 A MAAAADDD MAAADDD DAYYYYY,messy embb numbering agrrrhhhhh Tanushree Tunstall 2022-01-16 18:34:49 +00:00
• 07aedfe286 added both test logo plots in one script Tanushree Tunstall 2022-01-16 15:00:54 +00:00
• efe6703673 attempted omitting snp from logo plot for OR Tanushree Tunstall 2022-01-16 14:45:39 +00:00
• 1244581cdd just added some minor tweaks for the logo plots with OR Tanushree Tunstall 2022-01-16 13:31:32 +00:00
• 9546355241 updated and tested logoP_snp.R. All done nicely Tanushree Tunstall 2022-01-15 13:17:26 +00:00
• 0334188801 adde tests scripts for logoP and logoP_snp.R Tanushree Tunstall 2022-01-14 16:10:49 +00:00
• f640087922 added logoP_snp.R and renamed logo_plots_func.R to logoP.R Tanushree Tunstall 2022-01-14 16:09:57 +00:00
• f27b536157 added option to remove empty positions from logo plot Tanushree Tunstall 2022-01-14 11:07:16 +00:00
• 4e2f5f35db added log option to function properly Tanushree Tunstall 2022-01-14 10:50:56 +00:00
• 3b7cea3c47 adding legend forlogo plot Tanushree Tunstall 2022-01-14 10:18:01 +00:00
• 426a5cb0b5 added logo_plot function and test to check it Tanushree Tunstall 2022-01-13 18:55:13 +00:00
• 344a74a9e1 saving work for logo plots Tanushree Tunstall 2022-01-13 18:53:47 +00:00
• 7cbd9b4996 added barebone notes for logo_plots_func.R Tanushree Tunstall 2022-01-12 17:59:02 +00:00
• 3f7bc908ec going through functions and script for interactive plots Tanushree Tunstall 2022-01-12 17:58:16 +00:00
• 1f266c4cb8 more tidying and formatting for combining_dfs.py. Hopefully no more after today Tanushree Tunstall 2022-01-11 17:51:28 +00:00
• c48fa1dbb0 minor tidy up to check interactive graphs Rshiny Tanushree Tunstall 2022-01-07 16:07:44 +00:00
• 7d60a09297 tidy up Tanushree Tunstall 2022-01-06 16:38:59 +00:00
• bffa3c376c thorough checking and updates for final running of all gene targets Tanushree Tunstall 2022-01-05 17:55:35 +00:00
• b66cf31219 added untracked files in scripts/plotting Tanushree Tunstall 2022-01-04 12:27:25 +00:00
• 3ab6a3dbc1 added untracked files in scripts and dynamut Tanushree Tunstall 2022-01-04 12:26:54 +00:00
• 00b84ccb1c handled rpob 5uhc position offset in mcsm_ppi2 Tanushree Tunstall 2022-01-04 10:45:29 +00:00
• 46e2c93885 merged changes from the combining_dfs.py file from branch 'embb_dev' Tanushree Tunstall 2021-11-24 07:58:27 +00:00
• 727ca1ee76 fixed the duplicate colum problem by removing them from combining_dfs.py embb_dev Tanushree Tunstall 2021-11-24 07:57:20 +00:00
• e5aca5e24f fixed the duplicate colum problem by removing them from combining_dfs.py Tanushree Tunstall 2021-11-24 07:57:20 +00:00
• 4f52627740 Merge branch 'embb_dev' Tanushree Tunstall 2021-11-19 08:05:46 +00:00
• 6550be3350 added info re having run mcsm_na for RNAP Tanushree Tunstall 2021-11-19 07:51:13 +00:00
• 436bdafece added info re having run mcsm_na for RNAP Tanushree Tunstall 2021-11-19 07:51:13 +00:00
• 7fd5e2710d ran mcsm_na for rpob's RNAP complex i.e 5UHC Tanushree Tunstall 2021-11-19 07:48:42 +00:00
• 2925c89d11 ran mcsm_na for rpob's RNAP complex i.e 5UHC Tanushree Tunstall 2021-11-19 07:48:42 +00:00
• 69b8ba9d08 ran mcsm format for embb Tanushree Tunstall 2021-11-13 09:43:56 +00:00
• cee10cc540 ran mcsm format for embb Tanushree Tunstall 2021-11-13 09:43:56 +00:00
• c32de1bf0f Merge branch 'embb_dev' Tanushree Tunstall 2021-11-12 14:37:10 +00:00
• 45c48485f1 saving work after running combining_dfs.py Tanushree Tunstall 2021-11-12 14:16:48 +00:00
• 4eaa0b5d2b saving work after running combining_dfs.py Tanushree Tunstall 2021-11-12 14:16:48 +00:00
• 1ddc5045d5 added TESTING_plots.R Tanushree Tunstall 2021-11-09 13:55:21 +00:00
• dad8f526a2 added TESTING_plots.R Tanushree Tunstall 2021-11-09 13:55:21 +00:00
• 34ee2519d3 added FIXME and TODO related to alr in combinig_dfs.py Tanushree Tunstall 2021-11-09 13:23:50 +00:00
• a5c7e1e9dd added FIXME and TODO related to alr in combinig_dfs.py Tanushree Tunstall 2021-11-09 13:23:50 +00:00
• 246cd636a1 saving work in LSHTM_analysis before combining data for targets Tanushree Tunstall 2021-11-09 12:44:11 +00:00
• ddae107314 saving work in LSHTM_analysis before combining data for targets Tanushree Tunstall 2021-11-09 12:44:11 +00:00
• 63ec8a1c37 added split_csv_chain.sh for mCSM-NA analysis in scripts/ Tanushree Tunstall 2021-10-29 14:00:25 +01:00
• 80f73a3697 cherry-pick mcsm_na/run_format_results_mcsm_na.py from master to ensure consistency Tanushree Tunstall 2021-10-28 12:54:04 +01:00
• 8035308cdf cherry-pick mcsm_na/run_format_results_mcsm_na.py from master to ensure consistency Tanushree Tunstall 2021-10-28 12:54:04 +01:00
• 59337c7b71 pull in merged changes to mcsm_na/run_format_results_mcsm_na.py from master, including the merge fix gidb_dev Tanushree Tunstall 2021-10-28 12:48:00 +01:00
• e2bc1cdde1 Merge branch 'gidb_dev' (including merge conflict while after adding CLI arguments for mcsm_na/format_results_mcsm_na.py) Tanushree Tunstall 2021-10-28 12:45:39 +01:00
• 66d6364e99 pretending that we added the CLI arguments Tanushree Tunstall 2021-10-28 12:43:44 +01:00
• 9cfb32afb8 pretending that we added the CLI arguments Tanushree Tunstall 2021-10-28 12:43:44 +01:00
• 7d6087c82e saving ppi2 format script on embb_dev branch Tanushree Tunstall 2021-10-28 12:22:46 +01:00
• 45208f4c3d saving ppi2 format script on embb_dev branch Tanushree Tunstall 2021-10-28 12:22:46 +01:00
• e4661963ab saving work after embb branch merge Tanushree Tunstall 2021-10-28 12:15:29 +01:00
• 9c37dbee31 bring in embb stuff which was in the wrong branch Tanushree Tunstall 2021-10-28 11:18:13 +01:00
• 3368e949e8 bring in embb stuff which was in the wrong branch Tanushree Tunstall 2021-10-28 11:18:13 +01:00
• c2f9ca62a9 much development Tanushree Tunstall 2021-10-28 10:41:43 +01:00
• 057291a561 much development Tanushree Tunstall 2021-10-28 10:41:43 +01:00
• 4639688922 added gene.lower to dynamut2 format result script Tanushree Tunstall 2021-10-19 11:12:34 +01:00
• 873fd3a121 added gene.lower to dynamut2 format result script Tanushree Tunstall 2021-10-19 11:12:34 +01:00
• 9ed9e703d6 added notes Tanushree Tunstall 2021-10-18 13:58:06 +01:00
• ba21188bd2 added notes Tanushree Tunstall 2021-10-18 13:58:06 +01:00
• a67a07db2d added cmd option for dynamut2 formatting results Tanushree Tunstall 2021-10-18 13:52:29 +01:00
• 675b222181 added cmd option for dynamut2 formatting results Tanushree Tunstall 2021-10-18 13:52:29 +01:00
• c5c4d74acf fixed output filename in deepddg_format.py Tanushree Tunstall 2021-09-30 13:37:17 +01:00
• 98325d763f fixed output filename in deepddg_format.py Tanushree Tunstall 2021-09-30 13:37:17 +01:00
• e6539461a3 moved deepddg_format.py from ind output dir to scripts Tanushree Tunstall 2021-09-30 13:35:33 +01:00
• af227f9864 moved deepddg_format.py from ind output dir to scripts Tanushree Tunstall 2021-09-30 13:35:33 +01:00
• 2eab87da62 fix runFoldx so that it looks for a missing rotabase.txt in the process_dir and also print the foldx command that will be run Tanushree Tunstall 2021-09-29 18:24:06 +01:00
• 93a91518e1 fix runFoldx so that it looks for a missing rotabase.txt in the process_dir and also print the foldx command that will be run Tanushree Tunstall 2021-09-29 18:24:06 +01:00
• 68288a0efd added separate script for splitting csv after adding chain ID. saves lots of post processing Tanushree Tunstall 2021-09-20 16:13:15 +01:00
• d443ecea6b added separate script for splitting csv after adding chain ID. saves lots of post processing Tanushree Tunstall 2021-09-20 16:13:15 +01:00
• f4ebb07045 split csv for isoniazid Tanushree Tunstall 2021-09-20 16:12:45 +01:00
• daa3556ede split csv for isoniazid Tanushree Tunstall 2021-09-20 16:12:45 +01:00
• 903b61e6ea saving minor update to function fix Tanushree Tunstall 2021-09-17 13:35:48 +01:00
• 5cd6c300a7 saving minor update to function fix Tanushree Tunstall 2021-09-17 13:35:48 +01:00
• b05f520081 fixed lf_bp function with aes_string and reformulate Tanushree Tunstall 2021-09-17 13:33:19 +01:00
• e115c3636c fixed lf_bp function with aes_string and reformulate Tanushree Tunstall 2021-09-17 13:33:19 +01:00
• 92fd905dea minor bug fixes to allow i_graps for stability to render correctly Tanushree Tunstall 2021-09-16 18:59:02 +01:00
• e2d7a6567e minor bug fixes to allow i_graps for stability to render correctly Tanushree Tunstall 2021-09-16 18:59:02 +01:00
• 1f7eb6483d sorting out bp_subcolours in interaction Tanushree Tunstall 2021-09-16 12:44:42 +01:00
• 51aa321792 sorting out bp_subcolours in interaction Tanushree Tunstall 2021-09-16 12:44:42 +01:00
• 60adbe25fb sorted merged_df2 and consequently others by position in combining_dfs_plotting.R Tanushree Tunstall 2021-09-16 12:43:36 +01:00
• e8734b1c4b sorted merged_df2 and consequently others by position in combining_dfs_plotting.R Tanushree Tunstall 2021-09-16 12:43:36 +01:00
• 46ebed6b3e corrected foldx_outcome classification in combining_dfs.py as positive are Destabilising and neg as Stabilising Tanushree Tunstall 2021-09-16 10:59:55 +01:00
• cb5d7aa5ab corrected foldx_outcome classification in combining_dfs.py as positive are Destabilising and neg as Stabilising Tanushree Tunstall 2021-09-16 10:59:55 +01:00