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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tidied script plotting_data.R by removing superceded code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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eb19efd287
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added stat_bp_stability.R which needs to be a function for generating stat plots
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2021-08-26 16:37:56 +01:00 |
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e36e7736db
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playing with dm_om (other)plots data and graph on gid branch
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2021-08-26 16:35:46 +01:00 |
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1e3670f935
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added log10 OR and P values to myaf_or_calcs.R
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2021-08-23 20:01:01 +01:00 |
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0c16937b68
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added corr plots as function for interactive graphs on shiny
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2021-08-20 18:52:47 +01:00 |
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c0c30fd527
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adde format_results_dynamut2.py and ran shiny scripts for barplots
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2021-08-19 16:25:38 +01:00 |
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9cb33ed67b
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added pdb_fasta_plot.R for generating some useful plots for shiny
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2021-08-17 10:55:06 +01:00 |
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067fc85163
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extracting gid seq from pdb file using pdbtools
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2021-08-17 10:53:26 +01:00 |
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9b1d1d009d
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added aa_index/ with script that return dfs for plots for shiny perhaps
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2021-08-13 16:22:11 +01:00 |
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1ea42097ae
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added dynamut results formatting scripts, althouh needs to be rerun once b7 completes
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2021-08-13 13:24:22 +01:00 |
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2e9d142184
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indicated f for format for mcms_na formatting script
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2021-08-13 13:23:42 +01:00 |
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2eee69ee80
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saving work
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2021-08-12 17:37:56 +01:00 |
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938dba7fcc
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extracted results for dynamut gid bissection b10_21
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2021-08-12 17:35:12 +01:00 |
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59a370b45a
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Merge branch 'master' into gidb_dev
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2021-08-12 15:35:28 +01:00 |
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3086972480
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minor tidy up for script submit_dynamut
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2021-08-12 15:33:57 +01:00 |
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a641347f63
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reran b7 since previous run file output was 0 bytes
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2021-08-12 15:29:36 +01:00 |
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e48f215227
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ran b9 and b10 for gid after Dynamut team reran due to server issues
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2021-08-12 10:06:43 +01:00 |
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96277d78f6
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saving dynamut and mcsm_na jobs submitted and retrieved
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2021-08-11 17:32:15 +01:00 |
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7c0824d0f2
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added script for formatting mcsm_na results
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2021-08-06 19:12:57 +01:00 |
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656639e871
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ran submit and get_results for one last batch for mcsm_na and did some bash formatting to get proper filenames, etc.
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2021-08-06 19:09:29 +01:00 |
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718f92d7ff
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resuming work after conference
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2021-08-05 16:54:34 +01:00 |
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6759649c61
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indicated which cols are not available for pnca as I ran these scripts for generating plots for the poster
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2021-07-07 13:12:29 +01:00 |
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5eb07cdf86
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added leg_title size for bp function
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2021-07-07 13:11:13 +01:00 |
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4bf4650c88
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generated pncA plot for poster for ps_combined
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2021-07-07 11:38:07 +01:00 |
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