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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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a5c7e1e9dd
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added FIXME and TODO related to alr in combinig_dfs.py
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2021-11-09 13:23:50 +00:00 |
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ddae107314
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saving work in LSHTM_analysis before combining data for targets
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2021-11-09 12:44:11 +00:00 |
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63ec8a1c37
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added split_csv_chain.sh for mCSM-NA analysis in scripts/
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2021-10-29 14:00:25 +01:00 |
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8035308cdf
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cherry-pick mcsm_na/run_format_results_mcsm_na.py from master to ensure consistency
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2021-10-28 12:54:04 +01:00 |
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e2bc1cdde1
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Merge branch 'gidb_dev' (including merge conflict while after adding CLI arguments for mcsm_na/format_results_mcsm_na.py)
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2021-10-28 12:45:39 +01:00 |
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9cfb32afb8
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pretending that we added the CLI arguments
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2021-10-28 12:43:44 +01:00 |
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45208f4c3d
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saving ppi2 format script on embb_dev branch
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2021-10-28 12:22:46 +01:00 |
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e4661963ab
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saving work after embb branch merge
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2021-10-28 12:15:29 +01:00 |
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3368e949e8
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bring in embb stuff which was in the wrong branch
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2021-10-28 11:18:13 +01:00 |
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057291a561
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much development
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2021-10-28 10:41:43 +01:00 |
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873fd3a121
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added gene.lower to dynamut2 format result script
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2021-10-19 11:12:34 +01:00 |
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ba21188bd2
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added notes
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2021-10-18 13:58:06 +01:00 |
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675b222181
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added cmd option for dynamut2 formatting results
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2021-10-18 13:52:29 +01:00 |
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98325d763f
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fixed output filename in deepddg_format.py
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2021-09-30 13:37:17 +01:00 |
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af227f9864
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moved deepddg_format.py from ind output dir to scripts
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2021-09-30 13:35:33 +01:00 |
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93a91518e1
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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
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2021-09-29 18:24:06 +01:00 |
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d443ecea6b
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added separate script for splitting csv after adding chain ID. saves lots of post processing
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2021-09-20 16:13:15 +01:00 |
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daa3556ede
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split csv for isoniazid
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2021-09-20 16:12:45 +01:00 |
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5cd6c300a7
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saving minor update to function fix
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2021-09-17 13:35:48 +01:00 |
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e115c3636c
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fixed lf_bp function with aes_string and reformulate
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2021-09-17 13:33:19 +01:00 |
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e2d7a6567e
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minor bug fixes to allow i_graps for stability to render correctly
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2021-09-16 18:59:02 +01:00 |
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51aa321792
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sorting out bp_subcolours in interaction
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2021-09-16 12:44:42 +01:00 |
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e8734b1c4b
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sorted merged_df2 and consequently others by position in combining_dfs_plotting.R
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2021-09-16 12:43:36 +01:00 |
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cb5d7aa5ab
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corrected foldx_outcome classification in combining_dfs.py as positive are Destabilising and neg as Stabilising
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2021-09-16 10:59:55 +01:00 |
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56600ac3f8
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added config/ with drug gene names
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2021-09-16 10:05:28 +01:00 |
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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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96e6e8db5d
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saving work and tidying script
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2021-09-15 19:37:39 +01:00 |
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f0e66b2f7b
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added the scratch script as _v2 to play while repurposing bp_subcolours.R
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2021-09-15 19:34:24 +01:00 |
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2ac5ec410e
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added test_bp_subcolours.R
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2021-09-15 19:33:52 +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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bf432cd054
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more updates to pairs_panels to take colnames for plotting
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2021-09-14 18:20:12 +01:00 |
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b98977336c
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updated my_pairs_panel.R to make the dots coloured
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2021-09-14 15:36:05 +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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27f0b15d4c
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tidied script plotting_data.R by removing superceded code
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2021-09-10 18:19:56 +01:00 |
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3ddbee8c90
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finally moved foldx_outcome and deepddg_outcome calcs to combine_dfs.py in python script i.e cleaned source data
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2021-09-10 18:19:01 +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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dda5d1ea93
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moved old lineage_dist plot scripts to redundant
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2021-09-09 16:16:18 +01:00 |
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2bd85f7021
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added lineage_dist_plots.R
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2021-09-09 16:15:07 +01:00 |
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93038fa17c
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added lineage_dist.R nad renamed lineage_bp_data file to lineage_data
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2021-09-09 16:14:14 +01:00 |
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b7d50fbbcd
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added lineage_labels and mutation_info_labels to combinig_dfs_plotting
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2021-09-09 16:10:11 +01:00 |
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03031d2eb6
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moved all test scripts for functions to tests/
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2021-09-09 13:12:07 +01:00 |
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2ee66c770b
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updated notes
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2021-09-07 11:18:10 +01:00 |
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686fd0cd80
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updated running_plotting_scripts.R
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2021-09-07 11:16:41 +01:00 |
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c9519b3b56
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moved old lineage_basic_barplot.R to redundant
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2021-09-07 10:52:26 +01:00 |
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3cee341170
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replaced old lineage barplot with count and diversity combined plots sourced from function
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2021-09-07 09:27:47 +01:00 |
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