From efe67036736f51b1bec352fbf710bb3b727e93aa Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sun, 16 Jan 2022 14:45:39 +0000
Subject: [PATCH] attempted omitting snp from logo plot for OR

---
 scripts/functions/logoP.R            | 25 ++++++++++---------------
 scripts/functions/logoP_snp.R        |  3 ---
 scripts/functions/tests/test_logoP.R |  7 ++-----
 3 files changed, 12 insertions(+), 23 deletions(-)

diff --git a/scripts/functions/logoP.R b/scripts/functions/logoP.R
index d25fd24..3066d9c 100644
--- a/scripts/functions/logoP.R
+++ b/scripts/functions/logoP.R
@@ -49,22 +49,17 @@ LogoPlotCustomH <- function(plot_df
                      , symbol_colname = "mutant_type"
                      , y_axis_log  = F
                      , log_value = log10
-                     , y_scale_increment = 5
-                     , rm_empty_pos = F
+                     , y_axis_increment = 5
+                     , rm_empty_y = F
                      , my_logo_col = "chemistry" 
                      , x_lab = "Position"
                      , y_lab = "Odds Ratio"
                      , x_ats = 12 # text size
                      , x_tangle = 90 # text angle
-                     #, theme_bgc
-                     #, xfont_bgc
-                     #, yfont_bgc
                      , y_ats = 22
                      , y_tangle = 0
                      , x_tts = 20 # title size
                      , y_tts = 23
-                     #, xtt_col = 
-                     #, ytt_col = 
                      , leg_pos = "none" # can be top, left, right and bottom or c(0.8, 0.9)
                      , leg_dir = "horizontal" #can be vertical or horizontal
                      , leg_ts = 15 # leg text size
@@ -75,7 +70,7 @@ LogoPlotCustomH <- function(plot_df
    #################################
    # Data processing for logo plot
    #################################
-    if (rm_empty_pos){
+   if (rm_empty_y){
       plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
       cat("\nRemoving empty positions...\n")
       }else{
@@ -83,8 +78,8 @@ LogoPlotCustomH <- function(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)
+    cat("\nRemoving y scale incremenet:", y_axis_increment)
+    y_lim = round_any(y_max, y_axis_increment, f = ceiling)
     
     #-------------------
     # logo data: LogOR
@@ -99,10 +94,10 @@ LogoPlotCustomH <- function(plot_df
     
     #!!! 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_axis_increment = 
+    #cat("\nRemoving y scale incremenet:", y_axis_increment)
     
-    #y_lim = round_any(y_max, y_scale_increment, f = ceiling)
+    #y_lim = round_any(y_max, y_axis_increment, f = ceiling)
     
     } else {
       
@@ -184,8 +179,8 @@ LogoPlotCustomH <- function(plot_df
                      , 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)
+                       , breaks = seq(0, (y_lim), by = y_axis_increment)
+                       #, labels = seq(0, (y_lim), by = y_axis_increment)
                        , limits = c(0, y_lim))
     if (y_axis_log){
       
diff --git a/scripts/functions/logoP_snp.R b/scripts/functions/logoP_snp.R
index 52eeafa..fa01541 100644
--- a/scripts/functions/logoP_snp.R
+++ b/scripts/functions/logoP_snp.R
@@ -23,7 +23,6 @@ LogoPlotSnps <- function(plot_df
                      , symbol_mut_colname = "mutant_type"
                      , symbol_wt_colname = "mutant_type"
                      , omit_snp_count = c(0)  # can be 1, 2, etc.
-                     
                      , my_logo_col = "chemistry" 
                      , x_lab = "Position"
                      , y_lab = "Count"
@@ -52,8 +51,6 @@ LogoPlotSnps <- function(plot_df
   max_mut = max(table(plot_df[[x_axis_colname]]))
   
   # Subset Data as specified by user
-  pos_freqC = c(1:max_mut)
-  
   cat("\nDisplaying nsSNP position frequency:\n")
   print(table(plot_df$mut_pos_occurrence))
   
diff --git a/scripts/functions/tests/test_logoP.R b/scripts/functions/tests/test_logoP.R
index 006c43e..9daeb42 100644
--- a/scripts/functions/tests/test_logoP.R
+++ b/scripts/functions/tests/test_logoP.R
@@ -1,17 +1,14 @@
-
 #source("~/git/LSHTM_analysis/config/gid.R")
 #source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
-
 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
-                            , y_scale_increment = 5
-                 
-                            , rm_empty_pos = F
+                            , y_axis_increment = 5
+                            , rm_empty_y = T
                             , my_logo_col = 'chemistry'
                             , x_lab = "Position"
                             , y_lab = "Odds Ratio"