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sorting the ensemble and priority for ligand affinity

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This commit is contained in:
Tanushree Tunstall 2022-08-01 13:36:05 +01:00
parent f3710bfaf5
commit 79c261963b
2 changed files with 66 additions and 59 deletions
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51
scripts/plotting/mcsm_mean_stability_ensemble.R
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@ -1,4 +1,4 @@
source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/alr.R")
#source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/embb.R")
@ -57,38 +57,33 @@ common_cols = c("mutationinformation"
, "sensitivity"
, "ligand_distance")
# ADD the ones for mcsm_na etc
#optional_cols = c()
all_colnames$`colnames(df3)`[grep("scaled", all_colnames$`colnames(df3)`)]
scaled_cols = c("duet_scaled" , "duet_stability_change"
,"deepddg_scaled" , "deepddg"
,"ddg_dynamut2_scaled" , "ddg_dynamut2"
,"foldx_scaled" , "ddg_foldx"
, "deepddg_scaled" , "deepddg"
, "ddg_dynamut2_scaled" , "ddg_dynamut2"
, "foldx_scaled" , "ddg_foldx"
, "affinity_scaled" , "ligand_affinity_change"
, "mmcsm_lig_scaled" , "mmcsm_lig"
, "mcsm_ppi2_scaled" , "mcsm_ppi2_affinity"
, "mcsm_na_scaled" , "mcsm_na_affinity"
#,"consurf_scaled" , "consurf_score"
#,"snap2_scaled" , "snap2_score"
#,"provean_scaled" , "provean_score"
#,"affinity_scaled" , "ligand_affinity_change"
#,"mmcsm_lig_scaled" , "mmcsm_lig"
)
#, "consurf_scaled" , "consurf_score"
#, "snap2_scaled" , "snap2_score"
#, "provean_scaled" , "provean_score"
)
all_colnames$`colnames(df3)`[grep("outcome", all_colnames$`colnames(df3)`)]
outcome_cols = c("duet_outcome"
, "deepddg_outcome"
, "ddg_dynamut2_outcome"
, "foldx_outcome"
#, "ddg_foldx", "foldx_scaled"
# consurf outcome doesn't exist
#,"provean_outcome"
#,"snap2_outcome"
#,"ligand_outcome"
#,"mmcsm_lig_outcome"
#, "mcsm_ppi2_outcome"
#, "mcsm_na_outcome"
)
outcome_cols_aff = c("duet_outcome"
, "deepddg_outcome"
, "ddg_dynamut2_outcome"
, "foldx_outcome"
#, "ddg_foldx", "foldx_scaled"
, "ligand_outcome"
, "mmcsm_lig_outcome"
, "mcsm_ppi2_outcome"
, "mcsm_na_outcome"
# consurf outcome doesn't exist
#,"provean_outcome"
#,"snap2_outcome"
)
cols_to_consider = colnames(df3)[colnames(df3)%in%c(common_cols, scaled_cols,outcome_cols)]
cols_to_extract = cols_to_consider[cols_to_consider%in%c(common_cols, outcome_cols)]