consurf plot: add debug option. logoP SNP: distance flame tiles

scripts/functions/consurfP.R

@@ -86,6 +86,7 @@ wideP_consurf <- function(plotdf
                           , tpos3 = 0
                           
                           , default_gt_clr = "white"
+                          , debug=FALSE
 ){
   
   if(missing(point_colours)){
@@ -460,10 +461,12 @@ wideP_consurf <- function(plotdf
     if (all(!is.null(active_aa_pos) &&
             !is.null(aa_pos_drug) &&
             !is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && !is.null(aa_pos_lig3))) {
+      if (debug){
         cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2&3 sites")
         cat("\nCreating column colours, column name:", aa_colour_colname3)
         
         cat("\nDoing Plot with 3 ligands")
+      }
       out = out +  geom_tile(aes(,tpos3
                                  , width  = tW
                                  , height = tH )
@@ -483,19 +486,22 @@ wideP_consurf <- function(plotdf
                   , fill = plotdf[[aa_colour_colname1]]
                   , colour = plotdf[[aa_colour_colname1]]
                   , linetype = "solid")
-    
+      if (debug){
         cat("\nDone Plot with 3 ligands")
       }
+    }
     #---------------------
     # Add2plot: 2 ligands
     #---------------------
     if (all(!is.null(active_aa_pos) &&
             !is.null(aa_pos_drug) &&
             !is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
+      if (debug){
       cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2 sites")
       cat("\nCreating column colours, column name:", aa_colour_colname2)
       
       cat("\nDoing Plot with 2 ligands")
+      }
       out = out + 
         geom_tile(aes(, tpos2
                       , width  = tW
@@ -509,9 +515,10 @@ wideP_consurf <- function(plotdf
                   , fill = plotdf[[aa_colour_colname1]]
                   , colour = plotdf[[aa_colour_colname1]]
                   , linetype = "solid")
-      
+      if (debug){
       cat("\nDone Plot with 2 ligands")
       }
+    }
     
     #---------------------
     # Add2plot: 1 ligand
@@ -519,11 +526,12 @@ wideP_consurf <- function(plotdf
     if (all(!is.null(active_aa_pos) &&
             !is.null(aa_pos_drug) &&
             !is.null(aa_pos_lig1) && is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
+      if (debug){
       cat("\n\nAnnotating xvar with active, drug binding, and Lig 1 sites")
       cat("\nCreating column colours, column name:", aa_colour_colname1)
       
       cat("\nDoing Plot with 1 ligands")
-      
+      }
       out = out + 
         geom_tile(aes(, tpos1
                       , width  = tW
@@ -546,20 +554,20 @@ wideP_consurf <- function(plotdf
             is.null(aa_pos_lig1) &&
             is.null(aa_pos_lig2) &&
             is.null(aa_pos_lig3))) {
-      
+      if (debug){
       cat("\n\nAnnotating xvar with active and drug binding sites")
       cat("\nCreating column colours, column name:", aa_colour_colname)
       cat("\nDoing Plot with 0 ligands: active and drug site only")
-      
+      }
       out = out + geom_tile(aes(, tpos3
                                 , width  = tW
                                 , height = tH)
                             , fill = plotdf[[aa_colour_colname]]
                             , colour = plotdf[[aa_colour_colname]]
                             , linetype = "solid")
-      
+      if (debug){
       cat("\nDone Plot with: Active and Drug sites")
-      
+      }
     }
   }else{
     cat("\nNo annotation for additional ligands on xvar requested")

scripts/functions/logoP_snp.R

@@ -117,14 +117,16 @@ LogoPlotSnps <- function(plot_df
   
   if (is.matrix(tab_mt)){
     cat("\nPASS: Mutant matrix successfully created..."
-        , "\nRownames of mutant matrix:", rownames(tab_mt)
+        #, "\nRownames of mutant matrix:", rownames(tab_mt)
-        , "\nColnames of mutant matrix:", colnames(tab_mt))
+        #, "\nColnames of mutant matrix:", colnames(tab_mt)
+        )
   } else{
     tab_mt = as.matrix(tab_mt, rownames = T)
     if (is.matrix(tab_mt)){
       cat("\nCreating mutant matrix..."
-          , "\nRownames of mutant matrix:", rownames(tab_mt)
+          #, "\nRownames of mutant matrix:", rownames(tab_mt)
-          , "\nColnames of mutant matrix:", colnames(tab_mt))
+          #, "\nColnames of mutant matrix:", colnames(tab_mt)
+          )
     }
   }
   
@@ -151,8 +153,9 @@ LogoPlotSnps <- function(plot_df
         , "\nDim of wt matrix:", dim(tab_wt)
         , "\nDim of mutant matrix:", dim(tab_mt)
         , "\n"      
-        , "\nRownames of mutant matrix:", rownames(tab_wt)
+        #, "\nRownames of mutant matrix:", rownames(tab_wt)
-        , "\nColnames of mutant matrix:", colnames(tab_wt))
+        #, "\nColnames of mutant matrix:", colnames(tab_wt)
+        )
   }
 
   ######################################