renamed logoP.R --> logoP_or.R

scripts/functions/logoP_or.R

@@ -0,0 +1,190 @@
+#logo plots
+
+# create functions
+
+# one with OR
+  # --> select/drop down option to remove empty positions
+  # --> select/drop down option for colour
+      # --> if clustalx and taylor,  set variable to black bg + white font
+      # --> if chemistry and hydrophobicity, then grey bg +  black font 
+
+  # --> select/drop down option for log scale
+  # --> should include WT
+
+# one for multiple muts
+  # --> select/drop down option to filter count of nsSNPs
+  # --> select/drop down  option for colour
+  # --> should include WT
+
+# Make it hover over position and then get the corresponding data table!
+#%%======================================================================
+
+#==================
+# logo data: OR
+#==================
+# NOTE: my_logo_col
+# Can be one of these: 'chemistry', 'hydrophobicity', 'clustalx', 'taylor'
+# if 'chemistry' or 'hydrophobicity' --> then bg is grey with  black font (x, y and labels)
+# if 'clustalx'or 'taylor' --> then bg is black with white font (x, y and labels)
+    #, theme_bgc = 
+    #, xfont_bgc = 
+    #, yfont_bgc = 
+    #, xtt_col = 
+    #, ytt_col = 
+
+LogoPlotCustomH <- function(plot_df
+                     , x_axis_colname = "position"
+                     , y_axis_colname = "or_mychisq"
+                     , symbol_colname = "mutant_type"
+                     , y_axis_log  = F
+                     , log_value = log10
+                     , 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
+                     , y_ats = 22
+                     , y_tangle = 0
+                     , x_tts = 20 # title size
+                     , y_tts = 23
+                     , 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
+                     , leg_tts = 16 # leg title size
+                     )
+
+{
+   #################################
+   # 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")
+      }else{
+      plot_df = plot_df
+      }
+    
+    y_max = max(plot_df['or_mychisq'], na.rm = T)
+    cat("\nRemoving y scale incremenet:", y_axis_increment)
+    y_lim = round_any(y_max, y_axis_increment, f = ceiling)
+    
+    #-------------------
+    # 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)]
+    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_axis_increment = 
+    #cat("\nRemoving y scale incremenet:", y_axis_increment)
+    
+    #y_lim = round_any(y_max, y_axis_increment, f = ceiling)
+    
+    } 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))
+    
+  }
+
+  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
+  #####################################
+  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"
+    xtt_col    = "white"
+    ytt_col    = "white"
+  }
+
+  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"
+    xtt_col    = "black"
+    ytt_col    = "black"
+  }
+ 
+  p0 = ggseqlogo(logo_dfP_wf
+                      , method = "custom"
+                      , col_scheme = my_logo_col
+                      , seq_type = "aa") + 
+    #ylab("my custom height") +
+    theme(axis.text.x = element_text(size = x_ats
+                                      , angle = x_tangle
+                                      , hjust = 1
+                                      , vjust = 0.4
+                                      , colour = xfont_bgc)
+           , axis.text.y = element_text(size = y_ats
+                                        , angle = y_tangle
+                                        , hjust = 1
+                                        , vjust = 0
+                                        , colour = yfont_bgc)
+           , axis.title.x = element_text(size = x_tts
+                                        , colour = xtt_col)
+           , axis.title.y = element_text(size = y_tts
+                                        , colour = ytt_col)
+           , legend.title = element_text(size = leg_tts
+                                        , colour = ytt_col)
+           , legend.text = element_text(size = leg_ts)
+          
+           , legend.position = leg_pos
+           , legend.direction = leg_dir
+           , plot.background = element_rect(fill = theme_bgc))+
+    
+    scale_x_discrete(x_lab
+                     #, breaks
+                     , labels = position_or
+                     , limits = factor(1:length(position_or)))
+  
+    LogoPlot = p0 + scale_y_continuous(y_lab
+                       , 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){
+      
+      if (grepl("Log", y_lab)){
+        y_lab = y_lab
+        
+      }else{
+        y_lab = paste("Log", y_lab)
+      }
+      
+    LogoPlot = p0 + ylab(y_lab)
+  
+    }
+
+
+  return(LogoPlot)
+
+}