From 4e2f5f35dbb0c4f86ab24f1805864017dcd1147f Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 14 Jan 2022 10:50:56 +0000
Subject: [PATCH] added log option to function properly

---
 scripts/functions/logo_plots_func.R           | 71 ++++++++-----------
 .../functions/tests/test_logo_plots_func.R    |  9 +--
 2 files changed, 34 insertions(+), 46 deletions(-)

diff --git a/scripts/functions/logo_plots_func.R b/scripts/functions/logo_plots_func.R
index f4d1c4c..3146db4 100644
--- a/scripts/functions/logo_plots_func.R
+++ b/scripts/functions/logo_plots_func.R
@@ -43,11 +43,11 @@
 # ADD legend for hydrophobicity: done
 # ADD option to remove empty positions
 
-LogoPlotCustomH <- function(plotdf
+LogoPlotCustomH <- function(plot_df
                      , x_axis_colname = "position"
                      , y_axis_colname = "or_mychisq"
                      , symbol_colname = "mutant_type"
-                     , y_axis_log  = T
+                     , y_axis_log  = F
                      , log_value = log10
                      , my_logo_col = "chemistry" 
                      , x_lab = "Position"
@@ -73,52 +73,39 @@ LogoPlotCustomH <- function(plotdf
   #################################
   # Data processing for logo plot
   #################################
-  
-  logo_df = plotdf
-  
-  logo_data_plot2 = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
-  
-  #==================
-  # logo data: OR
-  #==================
-  logo_data_plot2_or = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
-  
-  wide_df2_or  =  as.matrix(logo_data_plot2_or %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
-  class(wide_df2_or)
-  
-  rownames(wide_df2_or) = wide_df2_or[,1]
-  dim(wide_df2_or)
-  
-  wide_df2_or = wide_df2_or[,-1]
-  str(wide_df2_or)
-  
-  colnames(wide_df2_or)
-  position_or = as.numeric(colnames(wide_df2_or))
-
-  #==================
-  # logo data: logOR
-  #==================
   if (y_axis_log){
     
+    #=====================
+    # logo data: LogOR
+    #=====================
     log_colname = paste0("log_", y_axis_colname)
-    logo_df[log_colname] = log_value(logo_df[y_axis_colname])
-    logo_data_plot2 = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname,log_colname )]
+    plot_df[log_colname] = log_value(plot_df[y_axis_colname])
+    logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)]
+    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))
     
-    logo_data_plot2_logor = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
-  
-    wide_df2_logor = as.matrix(logo_data_plot2_logor %>% spread(x_axis_colname, log_colname, fill = 0.0))
-    class(wide_df2_logor)
+    } 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))
     
-    rownames(wide_df2_logor) = wide_df2_logor[,1]
-    dim(wide_df2_logor)
-    
-    wide_df2_logor = wide_df2_logor[,-1]
-    str(wide_df2_logor)
-    
-    colnames(wide_df2_logor)
-    position_logor = as.numeric(colnames(wide_df2_logor))
   }
 
+  class(logo_dfP_wf)
+  
+  rownames(logo_dfP_wf) = logo_dfP_wf[,1]
+  dim(logo_dfP_wf)
+  
+  logo_dfP_wf = logo_dfP_wf[,-1]
+  str(logo_dfP_wf)
+  
+  colnames(logo_dfP_wf)
+  position_or = as.numeric(colnames(logo_dfP_wf))
+
   ######################################
   # Generating plots with given y_axis
   #####################################
@@ -144,7 +131,7 @@ LogoPlotCustomH <- function(plotdf
     ytt_col    = "black"
   }
  
-  LogoPlot = ggseqlogo(wide_df2_or
+  LogoPlot = ggseqlogo(logo_dfP_wf
                       , method = "custom"
                       , col_scheme = my_logo_col
                       , seq_type = "aa") + ylab("my custom height") +
diff --git a/scripts/functions/tests/test_logo_plots_func.R b/scripts/functions/tests/test_logo_plots_func.R
index d5f5083..391b5e2 100644
--- a/scripts/functions/tests/test_logo_plots_func.R
+++ b/scripts/functions/tests/test_logo_plots_func.R
@@ -3,24 +3,25 @@
 #source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
 
-LogoPlotCustomH (plotdf = merged_df3
+LogoPlotCustomH (plot_df = merged_df3
                             , x_axis_colname = "position"
                             , y_axis_colname = "or_mychisq"
                             , symbol_colname = "mutant_type"
                             , y_axis_log  = F
                             , log_value = log10
-                            , my_logo_col = 'chemistry'
+                            , my_logo_col = 'taylor'
                             , x_lab = "Position"
                             , y_lab = "Odds Ratio"
                             , x_ats = 12 # text size
                             , x_tangle = 90 # text angle
                             , y_ats = 22
                             , y_tangle = 0
-                            , x_tts = 20 # title size
-                            , y_tts = 23
+                            , x_tts = 19 # title size
+                            , y_tts = 22
                             #, leg_pos = c(0.05,-0.12)
                             , leg_pos = "top"
                             , leg_dir = "horizontal"
                             , leg_ts = 15 # leg text size
                             , leg_tts = 16 # leg title size
 )
+