combined msa and wt seq into 1 list so only list is passed as an arg for plotting ED plots

scripts/functions/consurfP.R

@@ -540,7 +540,7 @@ wideP_consurf <- function(plotdf
       
     }
   }else{
-    cat("\nNo annotation for xvar requested")
+    cat("\nNo annotation for additional ligands on xvar requested")
   } 
   #==============================================
   if (A_xvar_lig){

scripts/functions/logoP_msa.R

@@ -38,8 +38,9 @@
 
 
 ###########################################
-LogoPlotMSA <- function(msaSeq_mut # chr vector
-                        , msaSeq_wt # chr vector
+#LogoPlotMSA <- function(msaSeq_mut # chr vector
+#                        , msaSeq_wt # chr vector
+LogoPlotMSA <- function(unified_msa
                         , logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
                         , EDScore_type =  c("log") # see if this relevant, or source function should have it!
                         , bg_prob = NULL
@@ -64,7 +65,12 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector
                      )
 
 {
-  
+  # FIXME: Hack!
+  # msaSeq_mut=unified_msa[[1]]
+  # msaSeq_wt=unified_msa[[2]]
+  msaSeq_mut=unified_msa[['msa_seq']]
+  msaSeq_wt=unified_msa[['wt_seq']]
+
  # Get PFM matrix for mut and wt MSA provided
   data_ed = DataED_PFM(msaSeq_mut
                        , msaSeq_wt

scripts/functions/logoP_or.R

@@ -65,6 +65,7 @@ LogoPlotCustomH <- function(plot_df
    #################################
    # Data processing for logo plot
    #################################
+   
    if (rm_empty_y){
       plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
       cat("\nRemoving empty positions...\n")

scripts/functions/logoP_snp.R

@@ -54,7 +54,6 @@ LogoPlotSnps <- function(plot_df
    ############################################
    # Data processing for logo plot for nsSNPS
    ############################################
-
   setDT(plot_df)[, mut_pos_occurrence := .N, by = .(eval(parse(text=x_axis_colname)))] 
   
   table(plot_df[[x_axis_colname]])