|
|
63ec8a1c37
|
added split_csv_chain.sh for mCSM-NA analysis in scripts/
|
2021-10-29 14:00:25 +01:00 |
|
|
|
e2bc1cdde1
|
Merge branch 'gidb_dev' (including merge conflict while after adding CLI arguments for mcsm_na/format_results_mcsm_na.py)
|
2021-10-28 12:45:39 +01:00 |
|
|
|
9cfb32afb8
|
pretending that we added the CLI arguments
|
2021-10-28 12:43:44 +01:00 |
|
|
|
e4661963ab
|
saving work after embb branch merge
|
2021-10-28 12:15:29 +01:00 |
|
|
|
3368e949e8
|
bring in embb stuff which was in the wrong branch
|
2021-10-28 11:18:13 +01:00 |
|
|
|
057291a561
|
much development
|
2021-10-28 10:41:43 +01:00 |
|
|
|
873fd3a121
|
added gene.lower to dynamut2 format result script
|
2021-10-19 11:12:34 +01:00 |
|
|
|
ba21188bd2
|
added notes
|
2021-10-18 13:58:06 +01:00 |
|
|
|
675b222181
|
added cmd option for dynamut2 formatting results
|
2021-10-18 13:52:29 +01:00 |
|
|
|
98325d763f
|
fixed output filename in deepddg_format.py
|
2021-09-30 13:37:17 +01:00 |
|
|
|
af227f9864
|
moved deepddg_format.py from ind output dir to scripts
|
2021-09-30 13:35:33 +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
|
2021-09-29 18:24:06 +01:00 |
|
|
|
d443ecea6b
|
added separate script for splitting csv after adding chain ID. saves lots of post processing
|
2021-09-20 16:13:15 +01:00 |
|
|
|
daa3556ede
|
split csv for isoniazid
|
2021-09-20 16:12:45 +01:00 |
|
|
|
5cd6c300a7
|
saving minor update to function fix
|
2021-09-17 13:35:48 +01:00 |
|
|
|
e115c3636c
|
fixed lf_bp function with aes_string and reformulate
|
2021-09-17 13:33:19 +01:00 |
|
|
|
e2d7a6567e
|
minor bug fixes to allow i_graps for stability to render correctly
|
2021-09-16 18:59:02 +01:00 |
|
|
|
51aa321792
|
sorting out bp_subcolours in interaction
|
2021-09-16 12:44:42 +01:00 |
|
|
|
e8734b1c4b
|
sorted merged_df2 and consequently others by position in combining_dfs_plotting.R
|
2021-09-16 12:43:36 +01:00 |
|
|
|
cb5d7aa5ab
|
corrected foldx_outcome classification in combining_dfs.py as positive are Destabilising and neg as Stabilising
|
2021-09-16 10:59:55 +01:00 |
|
|
|
56600ac3f8
|
added config/ with drug gene names
|
2021-09-16 10:05:28 +01:00 |
|
|
|
746889b075
|
saving work for the day after massive repurpose
|
2021-09-15 19:48:56 +01:00 |
|
|
|
1d16c6848e
|
moved coloured_bp_data.R to redundant in light of updated function and reflected this in notes withing get_plotting_dfs.R
|
2021-09-15 19:42:08 +01:00 |
|
|
|
96e6e8db5d
|
saving work and tidying script
|
2021-09-15 19:37:39 +01:00 |
|
|
|
f0e66b2f7b
|
added the scratch script as _v2 to play while repurposing bp_subcolours.R
|
2021-09-15 19:34:24 +01:00 |
|
|
|
2ac5ec410e
|
added test_bp_subcolours.R
|
2021-09-15 19:33:52 +01:00 |
|
|
|
7550efbd4c
|
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
|
2021-09-15 19:29:09 +01:00 |
|
|
|
449af7acf4
|
fixed pos_count cals in function by specifying dplyr and changed summarize to summarise
|
2021-09-15 15:46:42 +01:00 |
|
|
|
bf432cd054
|
more updates to pairs_panels to take colnames for plotting
|
2021-09-14 18:20:12 +01:00 |
|
|
|
b98977336c
|
updated my_pairs_panel.R to make the dots coloured
|
2021-09-14 15:36:05 +01:00 |
|
|
|
996d67b423
|
added pretty colnames to corr_data.R
|
2021-09-13 10:24:41 +01:00 |
|
|
|
3f3fe89a6b
|
added shorter scripts for each different processing for plots to make it wasire to read code
|
2021-09-10 18:20:45 +01:00 |
|
|
|
27f0b15d4c
|
tidied script plotting_data.R by removing superceded code
|
2021-09-10 18:19:56 +01:00 |
|
|
|
3ddbee8c90
|
finally moved foldx_outcome and deepddg_outcome calcs to combine_dfs.py in python script i.e cleaned source data
|
2021-09-10 18:19:01 +01:00 |
|
|
|
5c8a9e8f00
|
sorted combining_dfs.py with all other data files and tidied up get_plotting_dfs.R
|
2021-09-10 18:16:41 +01:00 |
|
|
|
4ba4ff602e
|
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
|
2021-09-10 16:58:36 +01:00 |
|
|
|
dda5d1ea93
|
moved old lineage_dist plot scripts to redundant
|
2021-09-09 16:16:18 +01:00 |
|
|
|
2bd85f7021
|
added lineage_dist_plots.R
|
2021-09-09 16:15:07 +01:00 |
|
|
|
93038fa17c
|
added lineage_dist.R nad renamed lineage_bp_data file to lineage_data
|
2021-09-09 16:14:14 +01:00 |
|
|
|
b7d50fbbcd
|
added lineage_labels and mutation_info_labels to combinig_dfs_plotting
|
2021-09-09 16:10:11 +01:00 |
|
|
|
03031d2eb6
|
moved all test scripts for functions to tests/
|
2021-09-09 13:12:07 +01:00 |
|
|
|
2ee66c770b
|
updated notes
|
2021-09-07 11:18:10 +01:00 |
|
|
|
686fd0cd80
|
updated running_plotting_scripts.R
|
2021-09-07 11:16:41 +01:00 |
|
|
|
c9519b3b56
|
moved old lineage_basic_barplot.R to redundant
|
2021-09-07 10:52:26 +01:00 |
|
|
|
3cee341170
|
replaced old lineage barplot with count and diversity combined plots sourced from function
|
2021-09-07 09:27:47 +01:00 |
|
|
|
50b89cdcd7
|
one function with tuned params to generate count and diversity barplot
|
2021-09-06 19:52:56 +01:00 |
|
|
|
869fca7f94
|
added function for generating lineage barplots and also test script along wiadding script for processing data and added it to get_plotting_dfs.R
|
2021-09-06 19:50:50 +01:00 |
|
|
|
605eb54526
|
saving work for the day
|
2021-09-02 17:40:24 +01:00 |
|
|
|
a981580b7a
|
separated get_plotting_dfs_with_lig.R
|
2021-09-02 12:51:31 +01:00 |
|
|
|
fcb4b85747
|
modified bp with option for adding stats and boxplplots. Moved old one to redundant
|
2021-09-02 12:50:24 +01:00 |
|
