added outcome col to dm_om data

scripts/functions/dm_om_data.R

@@ -10,9 +10,10 @@
 # DistCutOff, LigDist_colname, ppi2Dist_colname, naDist_colname 
 
 dm_om_wf_lf_data <- function(df
-                          , gene_name               = gene # from globals
+                          , gene              # from globals
                           , colnames_to_extract
-                          , ligand_dist_colname     = LigDist_colname # from globals
+                          #, ligand_dist_colname     = LigDist_colname # from globals
+                          #, LigDist_colname # from globals used
                           #, ppi2Dist_colname #from globals used 
                           #, naDist_colname #from globals used
                           , dr_muts                 = dr_muts_col # from globals
@@ -52,11 +53,11 @@ dm_om_wf_lf_data <- function(df
   )
   
   # additional dfs
-  if (tolower(gene_name)%in%geneL_normal){
+  if (tolower(gene)%in%geneL_normal){
     wf_lf_dataL   = common_dfsL
   }
 
- if (tolower(gene_name)%in%geneL_na){
+ if (tolower(gene)%in%geneL_na){
     additional_dfL = list(
       wf_mcsm_na   = data.frame()
       , lf_mcsm_na = data.frame()
@@ -64,7 +65,7 @@ dm_om_wf_lf_data <- function(df
     wf_lf_dataL    = c(common_dfsL, additional_dfL)
   }
 
-  if (tolower(gene_name)%in%geneL_ppi2){
+  if (tolower(gene)%in%geneL_ppi2){
     additional_dfL   = list(
       wf_mcsm_ppi2   = data.frame()
       , lf_mcsm_ppi2 = data.frame()
@@ -248,6 +249,10 @@ if (nrow(lf_duet) == expected_rows_lf){
   quit()
 }
 
+# NEW columns [outcome and outcome colname]
+lf_duet$outcome_colname = "duet_outcome"
+lf_duet$outcome         = lf_duet$duet_outcome
+
 # Assign them to the output list
 wf_lf_dataL[['wf_duet']] = wf_duet
 wf_lf_dataL[['lf_duet']] = lf_duet
@@ -278,6 +283,10 @@ if (nrow(lf_foldx) == expected_rows_lf){
   quit()
 }
 
+# NEW column
+lf_foldx$outcome_colname = "foldx_outcome"
+lf_foldx$outcome         = lf_foldx$foldx_outcome
+
 # Assign them to the output list
 wf_lf_dataL[['wf_foldx']] = wf_foldx
 wf_lf_dataL[['lf_foldx']] = lf_foldx
@@ -308,6 +317,10 @@ if (nrow(lf_deepddg) == expected_rows_lf){
   quit()
 }
 
+# NEW columns [outcome and outcome colname]
+lf_deepddg$outcome_colname = "deepddg_outcome"
+lf_deepddg$outcome         = lf_deepddg$deepddg_outcome
+
 # Assign them to the output list
 wf_lf_dataL[['wf_deepddg']] = wf_deepddg
 wf_lf_dataL[['lf_deepddg']] = lf_deepddg
@@ -337,6 +350,10 @@ if (nrow(lf_dynamut2) == expected_rows_lf){
   quit()
 }
 
+# NEW columns [outcome and outcome colname]
+lf_dynamut2$outcome_colname = "ddg_dynamut2_outcome"
+lf_dynamut2$outcome         = lf_dynamut2$ddg_dynamut2_outcome
+
 # Assign them to the output list
 wf_lf_dataL[['wf_dynamut2']] = wf_dynamut2
 wf_lf_dataL[['lf_dynamut2']] = lf_dynamut2
@@ -384,6 +401,10 @@ if (nrow(lf_consurf) == expected_rows_lf){
   quit()
 }
 
+# NEW columns [outcome and outcome colname]
+lf_consurf$outcome_colname = "consurf_outcome"
+lf_consurf$outcome         = lf_consurf$consurf_outcome
+
 # Assign them to the output list
 wf_lf_dataL[['wf_consurf']] = wf_consurf
 wf_lf_dataL[['lf_consurf']] = lf_consurf
@@ -413,6 +434,10 @@ if (nrow(lf_snap2) == expected_rows_lf){
   quit()
 }
 
+# NEW columns [outcome and outcome colname]
+lf_snap2$outcome_colname = "snap2_outcome"
+lf_snap2$outcome         = lf_snap2$snap2_outcome
+
 # Assign them to the output list
 wf_lf_dataL[['wf_snap2']] = wf_snap2
 wf_lf_dataL[['lf_snap2']] = lf_snap2
@@ -442,6 +467,10 @@ if (nrow(lf_provean) == expected_rows_lf){
   quit()
 }
 
+# NEW columns [outcome and outcome colname]
+lf_provean$outcome_colname = "provean_outcome"
+lf_provean$outcome         = lf_provean$provean_outcome
+
 # Assign them to the output list
 wf_lf_dataL[['wf_provean']] = wf_provean
 wf_lf_dataL[['lf_provean']] = lf_provean
@@ -479,6 +508,10 @@ if (nrow(lf_mcsm_lig) == expected_rows_lf){
   quit()
 }
 
+# NEW columns [outcome and outcome colname]
+lf_mcsm_lig$outcome_colname = "ligand_outcome"
+lf_mcsm_lig$outcome         = lf_mcsm_lig$ligand_outcome
+
 # Assign them to the output list
 wf_lf_dataL[['wf_mcsm_lig']] = wf_mcsm_lig
 wf_lf_dataL[['lf_mcsm_lig']] = lf_mcsm_lig
@@ -487,7 +520,7 @@ wf_lf_dataL[['lf_mcsm_lig']] = lf_mcsm_lig
 # mcsm-NA affinity
 # data filtered by cut off
 #====================
-if (tolower(gene_name)%in%geneL_na){
+if (tolower(gene)%in%geneL_na){
   #---------------
   # mCSM-NA: WF and lF
   #-----------------
@@ -514,6 +547,10 @@ if (tolower(gene_name)%in%geneL_na){
     quit()
   }
   
+  # NEW columns [outcome and outcome colname]
+  lf_mcsm_na$outcome_colname = "mcsm_na_outcome"
+  lf_mcsm_na$outcome         = lf_mcsm_na$mcsm_na_outcome
+  
   # Assign them to the output list
   wf_lf_dataL[['wf_mcsm_na']] = wf_mcsm_na
   wf_lf_dataL[['lf_mcsm_na']] = lf_mcsm_na
@@ -524,7 +561,7 @@ if (tolower(gene_name)%in%geneL_na){
 # mcsm-ppi2 affinity
 # data filtered by cut off
 #========================
-if (tolower(gene_name)%in%geneL_ppi2){
+if (tolower(gene)%in%geneL_ppi2){
   #-----------------
   # mCSM-PPI2: WF and lF
   #-----------------
@@ -551,6 +588,10 @@ if (tolower(gene_name)%in%geneL_ppi2){
     quit()
   }
   
+  # NEW columns [outcome and outcome colname]
+  lf_mcsm_ppi2$outcome_colname = "mcsm_ppi2_outcome"
+  lf_mcsm_ppi2$outcome         = lf_mcsm_ppi2$mcsm_ppi2_outcome
+  
   # Assign them to the output list
   wf_lf_dataL[['wf_mcsm_ppi2']] = wf_mcsm_ppi2
   wf_lf_dataL[['lf_mcsm_ppi2']] = lf_mcsm_ppi2

scripts/functions/lf_bp2.R

@@ -7,7 +7,7 @@
 #############################
 
 lf_bp2 <- function(lf_df = lf_duet
-                   , p_title = "DUET-DDG"
+                   , p_title = ""
                    , colour_categ = "outcome"
                    , x_grp = "mutation_info_labels"
                    , y_var = "param_value"

scripts/plotting/get_plotting_dfs.R

@@ -117,7 +117,7 @@ geneL_normal  = c("pnca")
 geneL_na      = c("gid", "rpob")
 geneL_ppi2    = c("alr", "embb", "katg", "rpob")
 
-all_dm_om_df = dm_om_wf_lf_data(df = merged_df3, gene_name = gene)
+all_dm_om_df = dm_om_wf_lf_data(df = merged_df3, gene = gene)
 
 wf_duet      = all_dm_om_df[['wf_duet']]
 lf_duet      = all_dm_om_df[['lf_duet']]

scripts/plotting/plotting_thesis/dm_om_plots.R

@@ -1,3 +1,13 @@
+#################
+# Numbers
+##################
+nrow(wf_mcsm_lig)
+table(wf_mcsm_lig$mutation_info_labels)
+
+nrow(wf_mcsm_ppi2)
+table(wf_mcsm_ppi2$mutation_info_labels)
+################################################################
+
 geneL_normal  = c("pnca")
 geneL_na      = c("gid", "rpob")
 geneL_ppi2    = c("alr", "embb", "katg", "rpob")
@@ -116,6 +126,11 @@ stability_suffix <- paste0(delta_symbol, delta_symbol, "G")
 lf_bp2(lf_df_stabP, p_title = paste0("Stability",stability_suffix)
        , violin_quantiles = c(0.5), monochrome = F)
 
+lf_bp2(lf_duet, p_title = paste0("Stability",stability_suffix)
+       , violin_quantiles = c(0.5), monochrome = F)
+
+
+
 lf_bp2(lf_df_consP, p_title = "Evolutionary Conservation"
       , violin_quantiles = c(0.5), monochrome = F)