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59337c7b71
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pull in merged changes to mcsm_na/run_format_results_mcsm_na.py from master, including the merge fix
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2021-10-28 12:48:00 +01:00 |
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66d6364e99
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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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c2f9ca62a9
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much development
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2021-10-28 10:41:43 +01:00 |
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4639688922
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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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9ed9e703d6
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added notes
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2021-10-18 13:58:06 +01:00 |
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a67a07db2d
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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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c5c4d74acf
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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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e6539461a3
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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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2eab87da62
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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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68288a0efd
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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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f4ebb07045
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split csv for isoniazid
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2021-09-20 16:12:45 +01:00 |
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903b61e6ea
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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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b05f520081
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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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92fd905dea
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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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1f7eb6483d
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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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60adbe25fb
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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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46ebed6b3e
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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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c1d9781cb2
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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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d63980bb01
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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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c06b0eb696
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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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a5b6edab39
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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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6d542e7634
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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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1f19c26c2d
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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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5c252db1fa
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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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664d43f717
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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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6beb003de5
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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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036cc14e40
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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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1249a08fb9
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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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dc5b5e2f11
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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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96129ddc34
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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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c38462cf41
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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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e28be8bf0d
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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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4339976002
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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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9a18888f56
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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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f489b0625f
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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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66d45a8b73
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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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cdab8f0414
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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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9bb3ac2a01
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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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901f3896af
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updated notes
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2021-09-07 11:18:10 +01:00 |
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bc89534f64
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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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ebca0f4221
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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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7dc72fb118
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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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357ceb8920
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one function with tuned params to generate count and diversity barplot
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2021-09-06 19:52:56 +01:00 |
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7ba6868b60
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added function for generating lineage barplots and also test script along wiadding script for processing data and added it to get_plotting_dfs.R
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2021-09-06 19:50:50 +01:00 |
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343f867eed
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saving work for the day
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2021-09-02 17:40:24 +01:00 |
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55233ea474
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separated get_plotting_dfs_with_lig.R
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2021-09-02 12:51:31 +01:00 |
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2c65bb25d8
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modified bp with option for adding stats and boxplplots. Moved old one to redundant
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2021-09-02 12:50:24 +01:00 |
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c8e21b928c
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added functions for bp with stat and tested them
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2021-08-27 14:05:00 +01:00 |
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873049b603
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renamed dm_om barplot function scriptto lf_bp_stability.R
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2021-08-27 13:03:39 +01:00 |
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14d1ec84ab
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added function for stats from lf data
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2021-08-27 13:01:52 +01:00 |
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