From f27b536157d00a4373f92df6596a501bca3952bb Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 14 Jan 2022 11:07:16 +0000
Subject: [PATCH] added option to remove empty positions from logo plot

---
 scripts/functions/logo_plots_func.R           | 33 +++++++++++--------
 .../functions/tests/test_logo_plots_func.R    |  3 +-
 2 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/scripts/functions/logo_plots_func.R b/scripts/functions/logo_plots_func.R
index 3146db4..f28d434 100644
--- a/scripts/functions/logo_plots_func.R
+++ b/scripts/functions/logo_plots_func.R
@@ -49,6 +49,7 @@ LogoPlotCustomH <- function(plot_df
                      , symbol_colname = "mutant_type"
                      , y_axis_log  = F
                      , log_value = log10
+                     , rm_empty_pos = F
                      , my_logo_col = "chemistry" 
                      , x_lab = "Position"
                      , y_lab = "Odds Ratio"
@@ -70,14 +71,20 @@ LogoPlotCustomH <- function(plot_df
                      )
 
 {
-  #################################
-  # Data processing for logo plot
-  #################################
-  if (y_axis_log){
-    
-    #=====================
+   #################################
+   # Data processing for logo plot
+   #################################
+    if (rm_empty_pos){
+      plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
+      cat("\nRemoving empty positions...\n")
+      }else{
+      plot_df = plot_df
+      }
+    #-------------------
     # logo data: LogOR
-    #=====================
+    #-------------------
+    if (y_axis_log){
+    
     log_colname = paste0("log_", y_axis_colname)
     plot_df[log_colname] = log_value(plot_df[y_axis_colname])
     logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)]
@@ -86,9 +93,9 @@ LogoPlotCustomH <- function(plot_df
     
     } else {
       
-    #=====================
+    #-------------------
     # logo data: OR
-    #=====================
+    #-------------------
     logo_df = plot_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
     logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
     logo_dfP_wf  =  as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
@@ -109,11 +116,10 @@ LogoPlotCustomH <- function(plot_df
   ######################################
   # Generating plots with given y_axis
   #####################################
-  #if (my_logo_col == 'clustalx || taylor'){
-  
   if (my_logo_col %in% c('clustalx','taylor')) {
     cat("\nSelected colour scheme:", my_logo_col
         , "\nUsing black theme\n")
+    
     theme_bgc  = "black"
     xfont_bgc  = "white"
     yfont_bgc  = "white"
@@ -124,6 +130,7 @@ LogoPlotCustomH <- function(plot_df
   if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
     cat('\nSelected colour scheme:', my_logo_col
         , "\nUsing grey theme")
+    
     theme_bgc = "grey"
     xfont_bgc  = "black"
     yfont_bgc  = "black"
@@ -162,6 +169,4 @@ LogoPlotCustomH <- function(plot_df
   
   return(LogoPlot)
 
-}
-
-
+}
\ No newline at end of file
diff --git a/scripts/functions/tests/test_logo_plots_func.R b/scripts/functions/tests/test_logo_plots_func.R
index 391b5e2..b75ca9e 100644
--- a/scripts/functions/tests/test_logo_plots_func.R
+++ b/scripts/functions/tests/test_logo_plots_func.R
@@ -9,7 +9,8 @@ LogoPlotCustomH (plot_df = merged_df3
                             , symbol_colname = "mutant_type"
                             , y_axis_log  = F
                             , log_value = log10
-                            , my_logo_col = 'taylor'
+                            , rm_empty_pos = F
+                            , my_logo_col = 'hydrophobicity'
                             , x_lab = "Position"
                             , y_lab = "Odds Ratio"
                             , x_ats = 12 # text size