tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

added csv for all colnames

Browse source
This commit is contained in:
Tanushree Tunstall 2022-08-10 14:06:47 +01:00
parent 2f7558a883
commit ccc7dd7bf2
2 changed files with 255 additions and 0 deletions
Download patch file Download diff file Expand all files Collapse all files

156
scripts/plotting/plotting_thesis/colnames.csv Normal file
View file

@ -0,0 +1,156 @@
"colnames(merged_df3)"
"mutationinformation"
"id"
"sample"
"lineage"
"sublineage"
"country_code"
"drtype"
"ethambutol"
"mutation"
"drug_name"
"mutation_info"
"mutation_info_orig"
"mutation_info_v1"
"wild_type"
"mutant_type"
"position"
"Mut"
"Mut_copy"
"index_orig"
"index_orig_copy"
"snp_frequency"
"pos_count"
"wt_prop_water"
"mut_prop_water"
"wt_prop_polarity"
"mut_prop_polarity"
"wt_calcprop"
"mut_calcprop"
"total_id_ucount"
"maf"
"drtype_numeric"
"drtype_all_vals"
"drtype_all_names"
"drtype_multimode"
"drtype_mode"
"drtype_max"
"mutation_info_labels"
"dm_om_numeric"
"dm_om_numeric_orig"
"dst"
"dst_multimode"
"dst_mode"
"mutation_info_labels_v1"
"mutation_info_labels_orig"
"lineage_list_all"
"lineage_count_all"
"lineage_count_unique"
"lineage_list_unique"
"lineage_multimode"
"chain"
"ligand_id"
"ligand_distance"
"duet_stability_change"
"duet_outcome"
"ligand_affinity_change"
"ligand_outcome"
"duet_scaled"
"affinity_scaled"
"wild_pos"
"wild_chain_pos"
"ddg_foldx"
"contacts"
"electro_rr"
"electro_mm"
"electro_sm"
"electro_ss"
"disulfide_rr"
"disulfide_mm"
"disulfide_sm"
"disulfide_ss"
"hbonds_rr"
"hbonds_mm"
"hbonds_sm"
"hbonds_ss"
"partcov_rr"
"partcov_mm"
"partcov_sm"
"partcov_ss"
"vdwclashes_rr"
"vdwclashes_mm"
"vdwclashes_sm"
"vdwclashes_ss"
"volumetric_rr"
"volumetric_mm"
"volumetric_sm"
"volumetric_ss"
"foldx_scaled"
"foldx_outcome"
"deepddg"
"deepddg_outcome"
"deepddg_scaled"
"asa"
"rsa"
"ss"
"ss_class"
"kd_values"
"rd_values"
"wt_3upper"
"consurf_score"
"consurf_scaled"
"consurf_colour"
"consurf_colour_rev"
"consurf_ci_upper"
"consurf_ci_lower"
"consurf_ci_colour"
"consurf_msa_data"
"consurf_aa_variety"
"snap2_score"
"snap2_scaled"
"snap2_accuracy_pc"
"snap2_outcome"
"af"
"beta_logistic"
"or_logistic"
"pval_logistic"
"se_logistic"
"zval_logistic"
"ci_low_logistic"
"ci_hi_logistic"
"or_mychisq"
"log10_or_mychisq"
"or_fisher"
"pval_fisher"
"neglog_pval_fisher"
"ci_low_fisher"
"ci_hi_fisher"
"est_chisq"
"pval_chisq"
"ddg_dynamut2"
"ddg_dynamut2_scaled"
"ddg_dynamut2_outcome"
"mcsm_ppi2_affinity"
"mcsm_ppi2_scaled"
"mcsm_ppi2_outcome"
"interface_dist"
"mut_3upper"
"seq_offset4pdb"
"provean_score"
"provean_outcome"
"provean_scaled"
"mmcsm_lig"
"mmcsm_lig_scaled"
"mmcsm_lig_outcome"
"gene_name"
"pdb_file"
"lineage_labels"
"consurf_outcome"
"sensitivity"
"foldx_scaled_signC"
"avg_stability"
"avg_stability_outcome"
"avg_stability_scaled"
"avg_lig_affinity"
"avg_lig_affinity_outcome"
"avg_lig_affinity_scaled"
1 colnames(merged_df3)
2 mutationinformation
3 id
4 sample
5 lineage
6 sublineage
7 country_code
8 drtype
9 ethambutol
10 mutation
11 drug_name
12 mutation_info
13 mutation_info_orig
14 mutation_info_v1
15 wild_type
16 mutant_type
17 position
18 Mut
19 Mut_copy
20 index_orig
21 index_orig_copy
22 snp_frequency
23 pos_count
24 wt_prop_water
25 mut_prop_water
26 wt_prop_polarity
27 mut_prop_polarity
28 wt_calcprop
29 mut_calcprop
30 total_id_ucount
31 maf
32 drtype_numeric
33 drtype_all_vals
34 drtype_all_names
35 drtype_multimode
36 drtype_mode
37 drtype_max
38 mutation_info_labels
39 dm_om_numeric
40 dm_om_numeric_orig
41 dst
42 dst_multimode
43 dst_mode
44 mutation_info_labels_v1
45 mutation_info_labels_orig
46 lineage_list_all
47 lineage_count_all
48 lineage_count_unique
49 lineage_list_unique
50 lineage_multimode
51 chain
52 ligand_id
53 ligand_distance
54 duet_stability_change
55 duet_outcome
56 ligand_affinity_change
57 ligand_outcome
58 duet_scaled
59 affinity_scaled
60 wild_pos
61 wild_chain_pos
62 ddg_foldx
63 contacts
64 electro_rr
65 electro_mm
66 electro_sm
67 electro_ss
68 disulfide_rr
69 disulfide_mm
70 disulfide_sm
71 disulfide_ss
72 hbonds_rr
73 hbonds_mm
74 hbonds_sm
75 hbonds_ss
76 partcov_rr
77 partcov_mm
78 partcov_sm
79 partcov_ss
80 vdwclashes_rr
81 vdwclashes_mm
82 vdwclashes_sm
83 vdwclashes_ss
84 volumetric_rr
85 volumetric_mm
86 volumetric_sm
87 volumetric_ss
88 foldx_scaled
89 foldx_outcome
90 deepddg
91 deepddg_outcome
92 deepddg_scaled
93 asa
94 rsa
95 ss
96 ss_class
97 kd_values
98 rd_values
99 wt_3upper
100 consurf_score
101 consurf_scaled
102 consurf_colour
103 consurf_colour_rev
104 consurf_ci_upper
105 consurf_ci_lower
106 consurf_ci_colour
107 consurf_msa_data
108 consurf_aa_variety
109 snap2_score
110 snap2_scaled
111 snap2_accuracy_pc
112 snap2_outcome
113 af
114 beta_logistic
115 or_logistic
116 pval_logistic
117 se_logistic
118 zval_logistic
119 ci_low_logistic
120 ci_hi_logistic
121 or_mychisq
122 log10_or_mychisq
123 or_fisher
124 pval_fisher
125 neglog_pval_fisher
126 ci_low_fisher
127 ci_hi_fisher
128 est_chisq
129 pval_chisq
130 ddg_dynamut2
131 ddg_dynamut2_scaled
132 ddg_dynamut2_outcome
133 mcsm_ppi2_affinity
134 mcsm_ppi2_scaled
135 mcsm_ppi2_outcome
136 interface_dist
137 mut_3upper
138 seq_offset4pdb
139 provean_score
140 provean_outcome
141 provean_scaled
142 mmcsm_lig
143 mmcsm_lig_scaled
144 mmcsm_lig_outcome
145 gene_name
146 pdb_file
147 lineage_labels
148 consurf_outcome
149 sensitivity
150 foldx_scaled_signC
151 avg_stability
152 avg_stability_outcome
153 avg_stability_scaled
154 avg_lig_affinity
155 avg_lig_affinity_outcome
156 avg_lig_affinity_scaled

99
scripts/plotting/plotting_thesis/colnames_short.csv Normal file
View file

@ -0,0 +1,99 @@
"mutationinformation"
"id"
"lineage"
"drtype"
drug
"mutation"
"drug_name"
"mutation_info"
#"mutation_info_orig"
#"mutation_info_v1"
#"wild_type"
#"mutant_type"
#"position"
#"Mut"
"snp_frequency"
"pos_count"
"total_id_ucount"
"maf"
"drtype_mode"
"drtype_max"
"mutation_info_labels"
"dst"
"dst_mode"
#"mutation_info_labels_v1"
#"mutation_info_labels_orig"
"lineage_count_all"
"lineage_count_unique"
"chain"
"ligand_id"
LigDist_colname
"duet_stability_change"
"duet_outcome"
"ligand_affinity_change"
"ligand_outcome"
"duet_scaled"
"affinity_scaled"
"wild_pos"
"wild_chain_pos"
"ddg_foldx"
"foldx_scaled"
"foldx_outcome"
"deepddg"
"deepddg_outcome"
"deepddg_scaled"
"asa"
"rsa"
"ss"
"ss_class"
"kd_values"
"rd_values"
"wt_3upper"
"consurf_score"
"consurf_scaled"
"consurf_colour"
"consurf_colour_rev"
"consurf_ci_upper"
"consurf_ci_lower"
"consurf_ci_colour"
"consurf_msa_data"
"consurf_aa_variety"
"snap2_score"
"snap2_scaled"
"snap2_accuracy_pc"
"snap2_outcome"
"af"
"or_logistic"
"pval_logistic"
"or_mychisq"
"log10_or_mychisq"
"or_fisher"
"pval_fisher"
"neglog_pval_fisher"
"ddg_dynamut2"
"ddg_dynamut2_scaled"
"ddg_dynamut2_outcome"
"mcsm_ppi2_affinity"
"mcsm_ppi2_scaled"
"mcsm_ppi2_outcome"
ppi2Dist_colname
"mut_3upper"
"seq_offset4pdb"
"provean_score"
"provean_outcome"
"provean_scaled"
"mmcsm_lig"
"mmcsm_lig_scaled"
"mmcsm_lig_outcome"
"gene_name"
"pdb_file"
"lineage_labels"
"consurf_outcome"
"sensitivity"
"foldx_scaled_signC"
"avg_stability"
"avg_stability_outcome"
"avg_stability_scaled"
"avg_lig_affinity"
"avg_lig_affinity_outcome"
"avg_lig_affinity_scaled"
Can't render this file because it contains an unexpected character in line 9 and column 2.