From 1244581cddbd8cd60cbf4065b3a81ce3a63d8357 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sun, 16 Jan 2022 13:31:32 +0000
Subject: [PATCH] just added some minor tweaks for the logo plots with OR

---
 scripts/functions/logoP.R            | 45 +++++++++++++++++++++++-----
 scripts/functions/tests/test_logoP.R |  6 ++--
 2 files changed, 41 insertions(+), 10 deletions(-)

diff --git a/scripts/functions/logoP.R b/scripts/functions/logoP.R
index 1a18282..d25fd24 100644
--- a/scripts/functions/logoP.R
+++ b/scripts/functions/logoP.R
@@ -49,6 +49,7 @@ LogoPlotCustomH <- function(plot_df
                      , symbol_colname = "mutant_type"
                      , y_axis_log  = F
                      , log_value = log10
+                     , y_scale_increment = 5
                      , rm_empty_pos = F
                      , my_logo_col = "chemistry" 
                      , x_lab = "Position"
@@ -80,6 +81,11 @@ LogoPlotCustomH <- function(plot_df
       }else{
       plot_df = plot_df
       }
+    
+    y_max = max(plot_df['or_mychisq'], na.rm = T)
+    cat("\nRemoving y scale incremenet:", y_scale_increment)
+    y_lim = round_any(y_max, y_scale_increment, f = ceiling)
+    
     #-------------------
     # logo data: LogOR
     #-------------------
@@ -91,6 +97,13 @@ LogoPlotCustomH <- function(plot_df
     logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
     logo_dfP_wf  =  as.matrix(logo_df_plot %>% spread(x_axis_colname, log_colname, fill = 0.0))
     
+    #!!! For consideration: to add y_axis 'breaks' and 'limits' !!!
+    #y_max = max(plot_df[[log_colname]], na.rm = T)
+    #y_scale_increment = 
+    #cat("\nRemoving y scale incremenet:", y_scale_increment)
+    
+    #y_lim = round_any(y_max, y_scale_increment, f = ceiling)
+    
     } else {
       
     #-------------------
@@ -138,7 +151,7 @@ LogoPlotCustomH <- function(plot_df
     ytt_col    = "black"
   }
  
-  LogoPlot = ggseqlogo(logo_dfP_wf
+  p0 = ggseqlogo(logo_dfP_wf
                       , method = "custom"
                       , col_scheme = my_logo_col
                       , seq_type = "aa") + 
@@ -157,21 +170,37 @@ LogoPlotCustomH <- function(plot_df
                                         , colour = xtt_col)
            , axis.title.y = element_text(size = y_tts
                                         , colour = ytt_col)
-          , legend.title = element_text(size = y_tts
+           , legend.title = element_text(size = leg_tts
                                         , colour = ytt_col)
-          , legend.text = element_text(size = leg_ts)
+           , legend.text = element_text(size = leg_ts)
           
            , legend.position = leg_pos
            , legend.direction = leg_dir
-           , plot.background = element_rect(fill = theme_bgc)
-           , legend.text = element_text(size = leg_ts)
-           , legend.title = element_text(size = leg_tts))+
+           , plot.background = element_rect(fill = theme_bgc))+
+    
     scale_x_discrete(x_lab
                      #, breaks
                      , labels = position_or
-                     , limits = factor(1:length(position_or))) +
-    ylab(y_lab)
+                     , limits = factor(1:length(position_or)))
   
+    LogoPlot = p0 + scale_y_continuous(y_lab
+                       , breaks = seq(0, (y_lim), by = y_scale_increment)
+                       #, labels = seq(0, (y_lim), by = y_scale_increment)
+                       , limits = c(0, y_lim))
+    if (y_axis_log){
+      
+      if (grepl("Log", y_lab)){
+        y_lab = y_lab
+        
+      }else{
+        y_lab = paste("Log", y_lab)
+      }
+      
+    LogoPlot = p0 + ylab(y_lab)
+  
+    }
+
+
   return(LogoPlot)
 
 }
\ No newline at end of file
diff --git a/scripts/functions/tests/test_logoP.R b/scripts/functions/tests/test_logoP.R
index 57b9ac0..006c43e 100644
--- a/scripts/functions/tests/test_logoP.R
+++ b/scripts/functions/tests/test_logoP.R
@@ -7,9 +7,11 @@ LogoPlotCustomH (plot_df = merged_df3
                             , x_axis_colname = "position"
                             , y_axis_colname = "or_mychisq"
                             , symbol_colname = "mutant_type"
-                            , y_axis_log  = T
+                            , y_axis_log  = F
                             , log_value = log10
-                            , rm_empty_pos = T
+                            , y_scale_increment = 5
+                 
+                            , rm_empty_pos = F
                             , my_logo_col = 'chemistry'
                             , x_lab = "Position"
                             , y_lab = "Odds Ratio"