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gidb_dev

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• 0cc7a8fcae config: add tile stuff for all targets. Other functions: many rewrites! Tanushree Tunstall 2022-08-15 16:29:38 +01:00
• a3e5283a9b generated ggpairs plots finally Tanushree Tunstall 2022-08-15 19:05:22 +01:00
• b68841b337 saving work Tanushree Tunstall 2022-08-14 22:57:23 +01:00
• 7c40e13771 dadded v2 of barplot layput Tanushree Tunstall 2022-08-14 22:56:08 +01:00
• da8f8d90d4 removed setDT and replaced with dplyr alt in position_count_bp.R Tanushree Tunstall 2022-08-14 14:19:09 +01:00
• 65d697d3a2 saving work Tanushree Tunstall 2022-08-14 12:35:33 +01:00
• 939528024a turn off thing Tanushree Tunstall 2022-08-14 12:35:09 +01:00
• fcbf87705f gg_pairs_all: output to a png in /tmp Tanushree Tunstall 2022-08-14 12:20:13 +01:00
• 2acea43bcf added maf column in appendix_tables Tanushree Tunstall 2022-08-14 12:18:12 +01:00
• 6f354ab390 oops! Tanushree Tunstall 2022-08-14 12:17:36 +01:00
• c09d7530c9 added ORandSNP writing results Tanushree Tunstall 2022-08-13 21:19:40 +01:00
• 4609757efb added appendix tables script Tanushree Tunstall 2022-08-13 21:19:19 +01:00
• d984d283c5 generated embb lineage plots Tanushree Tunstall 2022-08-13 21:17:39 +01:00
• c8f3ddf892 colour changes Tanushree Tunstall 2022-08-13 15:40:25 +01:00
• c6a720770d some stuff Tanushree Tunstall 2022-08-12 10:03:32 +01:00
• 365c322953 added fd corrected p-values for ks stats Tanushree Tunstall 2022-08-13 14:54:51 +01:00
• f5f1e388c3 modified ks test to output all stats needed in one script Tanushree Tunstall 2022-08-12 14:35:03 +01:00
• 22be845e1f added ggpairs code Tanushree Tunstall 2022-08-12 10:04:35 +01:00
• 318941e91b older file renamed for prominent effects Tanushree Tunstall 2022-08-11 21:09:48 +01:00
• d6766d9d9c added plotting_colnames.R in scripts/plotting Tanushree Tunstall 2022-08-11 21:08:54 +01:00
• 1b08080078 added prominent_effects.R Tanushree Tunstall 2022-08-11 21:07:55 +01:00
• b32398d16f output corr plots with log10 labels Tanushree Tunstall 2022-08-11 21:03:27 +01:00
• 3d3e74306c added log10 to corr plot labels Tanushree Tunstall 2022-08-11 21:01:16 +01:00
• b302daaa60 rearranged corr plot cols and also added example for ggpairs Tanushree Tunstall 2022-08-11 20:56:34 +01:00
• fdb3f00503 added dist_mutation_to_na2.pl script from UQ to calculate dist to na Tanushree Tunstall 2022-08-11 10:09:33 +01:00
• e714034678 commented out test code Tanushree Tunstall 2022-08-10 20:03:40 +01:00
• 842efe4409 created prominent effect calcualtions Tanushree Tunstall 2022-08-10 20:02:20 +01:00
• 3af11ec3d3 wideP_consurf3 Tanushree Tunstall 2022-08-10 14:08:40 +01:00
• 0bcbb44ae5 addded old script to redundant Tanushree Tunstall 2022-08-10 14:08:08 +01:00
• ccc7dd7bf2 added csv for all colnames Tanushree Tunstall 2022-08-10 14:06:47 +01:00
• 2f7558a883 aadded colnames to plot as names Tanushree Tunstall 2022-08-10 14:06:13 +01:00
• 4315adc556 wideP_consurf3 Tanushree Tunstall 2022-08-10 14:07:11 +01:00
• f6a3b7f066 added lineage plots in one Tanushree Tunstall 2022-08-10 12:58:38 +01:00
• 285b28b1d6 various plots Tanushree Tunstall 2022-08-10 11:06:05 +01:00
• a6d93b3fa8 starting corr plots Tanushree Tunstall 2022-08-09 21:55:24 +01:00
• cd86fcf8e8 added separate scripts for layout for convinience Tanushree Tunstall 2022-08-09 21:47:24 +01:00
• d78b072732 comment out run Tanushree Tunstall 2022-08-09 20:00:42 +01:00
• 5ef9eb8826 saving Tanushree Tunstall 2022-08-09 19:58:32 +01:00
• faf9ab9707 various Tanushree Tunstall 2022-08-09 19:56:47 +01:00
• af03fc6fd6 various Tanushree Tunstall 2022-08-09 19:56:17 +01:00
• 415d05ab6e various stuff Tanushree Tunstall 2022-08-09 19:42:20 +01:00
• 5cbaef3d36 various heat-bar/position tile faff Tanushree Tunstall 2022-08-09 18:15:54 +01:00
• 94454d6fba added combined lineage plot Tanushree Tunstall 2022-08-09 19:33:49 +01:00
• fe292e3717 fix: add NULL for aa_pos_lig[123] for configs that don't have them Tanushree Tunstall 2022-08-09 13:51:05 +01:00
• 79d83b6240 various changes Tanushree Tunstall 2022-08-09 13:46:05 +01:00
• 4ce2087224 various changes Tanushree Tunstall 2022-08-08 16:48:40 +01:00
• 5bdfd03443 refactored dm om plots and generated the final layout Tanushree Tunstall 2022-08-08 16:45:55 +01:00
• 28510471f0 consurf tile fixes Tanushree Tunstall 2022-08-08 15:37:17 +01:00
• 0234a8f77b more plot modifications dm and om plots mainly Tanushree Tunstall 2022-08-08 15:32:16 +01:00
• 4e6f10d1ba added outcome col to dm_om data Tanushree Tunstall 2022-08-07 11:21:25 +01:00
• 54b3dd9d42 various refactoring Tanushree Tunstall 2022-08-06 18:48:49 +01:00
• c968089cd2 refactoring logo plots to add flame bar Tanushree Tunstall 2022-08-06 18:47:54 +01:00
• f0a9eb4eec aadded complete obs count for corr plots and added placeholder for mcsm-na Tanushree Tunstall 2022-08-06 14:31:18 +01:00
• f194b5ea4f added corr plot TODO for lineage counts Tanushree Tunstall 2022-08-06 13:30:41 +01:00
• 0e777108a9 saving and strating to write Tanushree Tunstall 2022-08-06 13:09:26 +01:00
• 569e372476 agenerated corr plots with MAF and provean Tanushree Tunstall 2022-08-06 13:08:42 +01:00
• 1a513913ce reflected the factor thing as been added as new additon Tanushree Tunstall 2022-08-05 20:00:04 +01:00
• fe9c3f8afe added dm_om_plots.R Tanushree Tunstall 2022-08-05 19:59:07 +01:00
• ae8bc8ae85 added as.factor in unpired stats Tanushree Tunstall 2022-08-05 19:58:31 +01:00
• 9c955cddc0 still playing Tanushree Tunstall 2022-08-05 18:49:26 +01:00
• 92fba43dc1 mods Tanushree Tunstall 2022-08-05 18:14:02 +01:00
• 57433607bc lf_bp2: add a "monochrome" option Tanushree Tunstall 2022-08-05 18:28:10 +01:00
• d5bc1c272e lf_bp2 Tanushree Tunstall 2022-08-05 18:13:44 +01:00
• 33925dafe9 things Tanushree Tunstall 2022-08-05 16:13:57 +01:00
• 6cb9998c4c added the script to redundant Tanushree Tunstall 2022-08-05 14:45:33 +01:00
• 164113f665 moved dm_om_data.R the script version to redundant and the function version has been trimmed to for readability Tanushree Tunstall 2022-08-05 14:44:36 +01:00
• cc27ffe82f added the rev script that i used to develop the trimmed version Tanushree Tunstall 2022-08-05 14:36:58 +01:00
• 05ab89ec09 git trimmed downthe dm_om_data.R Tanushree Tunstall 2022-08-05 14:36:02 +01:00
• fae846395d fix Tanushree Tunstall 2022-08-05 12:52:51 +01:00
• 31148dfbdc lf_bp fuckage Tanushree Tunstall 2022-08-05 12:46:14 +01:00
• c0f59bc9c9 breakage Tanushree Tunstall 2022-08-05 12:45:16 +01:00
• 14f8f5d6d4 generated lineage barplots and corr plots for conservation Tanushree Tunstall 2022-08-04 19:48:09 +01:00
• 424c1d184d added linage barplots Tanushree Tunstall 2022-08-04 19:29:20 +01:00
• 7f9facc1e6 moved old corr files Tanushree Tunstall 2022-08-04 19:28:39 +01:00
• dab8294a01 renamed folder Tanushree Tunstall 2022-08-04 18:52:03 +01:00
• ad2e538ec2 separated plotting_thesis for generating plots Tanushree Tunstall 2022-08-04 18:47:18 +01:00
• 95131abc3c consurf fixes Tanushree Tunstall 2022-08-04 16:48:37 +01:00
• bf41d01b39 multiple script updates and bug fixes Tanushree Tunstall 2022-08-04 16:48:17 +01:00
• 599cd7493f buggy bugs that bug me Tanushree Tunstall 2022-08-04 15:18:23 +01:00
• e1b8e103ea saving from my panino, made lineage dist plots Tanushree Tunstall 2022-08-04 13:46:58 +01:00
• 1efb534f0f fix some derps Tanushree Tunstall 2022-08-04 13:46:37 +01:00
• 61c7a30835 minor tidy and leble adjust sizes for simple barplots Tanushree Tunstall 2022-08-04 10:26:18 +01:00
• bcba0c359e moved code for structure figure to sep sir Tanushree Tunstall 2022-08-03 21:33:19 +01:00
• aabe466599 added plots for thesis Tanushree Tunstall 2022-08-03 21:32:47 +01:00
• 41c4996426 more of the previous thing Tanushree Tunstall 2022-08-03 20:51:32 +01:00
• bdbc97c40a fix many plot functions to stop them using the "g=ggplot()" pattern, which annoyingly throws away lots of useful data that RShiny needs for clickable plots. Also split the "flame bar" for ligand distance out into separate functions in generate_distance_colour_map.R. This can now be easily incorporated into any "wide" graph showing all positions. Tanushree Tunstall 2022-08-03 18:56:14 +01:00
• e498d46f8b consurf plot: add debug option. logoP SNP: distance flame tiles Tanushree Tunstall 2022-08-03 10:48:25 +01:00
• f2709f3992 added replace b factor scripts for lig affinity and ppi2 Tanushree Tunstall 2022-08-02 20:30:43 +01:00
• 87a3d7acf2 generated simple affinity plots for embb Tanushree Tunstall 2022-08-02 20:29:31 +01:00
• 214e9232c6 still trying affinity phew Tanushree Tunstall 2022-08-02 16:55:31 +01:00
• d94aa10c9b saving work Tanushree Tunstall 2022-08-01 21:44:11 +01:00
• 66337c289c added scripts to generate mean stability for rpob Tanushree Tunstall 2022-08-01 21:41:55 +01:00
• ccc877e811 attempting affintiy stuff Tanushree Tunstall 2022-08-01 21:41:02 +01:00
• 0d8979dfcb separted cols Tanushree Tunstall 2022-08-01 14:09:46 +01:00
• e750ee59aa saving Tanushree Tunstall 2022-08-01 13:41:43 +01:00
• 79c261963b sorting the ensemble and priority for ligand affinity Tanushree Tunstall 2022-08-01 13:36:05 +01:00
• f3710bfaf5 added mcsm_mean_affinity_ensemble.R and replaceBfactor_pdb_stability.R Tanushree Tunstall 2022-07-31 19:25:28 +01:00
• 1bf66b145c separating mcsm_mean_stability_ensemble from combined script Tanushree Tunstall 2022-07-31 19:24:35 +01:00
• 06e5363112 added scriptaa mcsm_mean_stability_ensemble.R to get ensemble of averages across predictors for stability and affinity Tanushree Tunstall 2022-07-31 16:29:47 +01:00
• 4de1e800ec moved mut_landscape files to plotting Tanushree Tunstall 2022-07-31 12:01:32 +01:00