added logo_plot function and test to check it

scripts/functions/logo_plots_func.R

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+#logo plots
+
+# create functions
+
+# one with OR
+  # --> select/drop down option to remove empty positions
+      # --> easy peasy, just select the merged_df3_comp
+  # --> 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
+
+# Data used
+#wide_df_or # or logo plot
+#wide_df_or_mult # > 1 sites
+#wide_df_logor_m #make it as a scale option. REDUNDANT
+#tab_mt # mutant logo plot
+#tab_wt # wt logo plot
+
+# 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
+# if 'clustalx'or 'taylor' --> then bg is black with white font
+    #, theme_bgc = 
+    #, xfont_bgc = 
+    #, yfont_bgc = 
+
+# ADD legend for hydrophobicity
+# ADD option to remove empty positions
+
+LogoPlotCustomH <- function(plotdf
+                     , x_axis_colname = "position"
+                     , y_axis_colname = "or_mychisq"
+                     , symbol_colname = "mutant_type"
+                     , y_axis_log  = T
+                     , log_value = log10
+                     , 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 = 25 # title size
+                     , y_tts = 20
+                     , leg_pos = "none"
+                     #, leg_pos = c(0.8, 0.9)
+                     , leg_ts = 15 # leg text size
+                     , leg_tts = 16 # leg title size
+                     )
+
+{
+  #################################
+  # Data processing for logo plot
+  #################################
+  
+  logo_df = plotdf
+  
+  if (y_axis_log){
+    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)]
+
+  #==================
+  # 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
+  #==================
+  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)
+  
+  rownames(wide_df2_logor) = wide_df2_logor[,1]
+  dim(wide_df2_logor)
+  
+  #wide_df2_logor = subset(wide_df_logor, select = -c(1) )
+  wide_df2_logor = wide_df2_logor[,-1]
+  str(wide_df2_logor)
+  
+  colnames(wide_df2_logor)
+  position_logor = as.numeric(colnames(wide_df2_logor))
+  
+
+  ######################################
+  # 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  = "black"
+    
+  }
+
+  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"
+    
+  }
+ 
+  LogoPlot = ggseqlogo(wide_df2_or
+                      , 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.y = element_text(size = x_tts)
+           , axis.title.x = element_text(size = y_tts)
+           #, legend.position = "bottom") + 
+           , legend.position = leg_pos
+           , plot.background = element_rect(fill = theme_bgc))+
+    #, legend.text = element_text(size = leg_ts)
+    #, legend.title = element_text(size = leg_tts))+
+    scale_x_discrete(x_lab
+                     #, breaks
+                     , labels = position_or
+                     , limits = factor(1:length(position_or))) +
+    ylab(y_lab)
+  
+  #print(logo_or)
+  return(LogoPlot)
+
+}
+
+

scripts/functions/tests/test_logo_plots_func.R

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+
+#source("~/git/LSHTM_analysis/config/gid.R")
+#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+
+
+LogoPlotCustomH (plotdf = merged_df3
+                            , x_axis_colname = "position"
+                            , y_axis_colname = "or_mychisq"
+                            , symbol_colname = "mutant_type"
+                            , y_axis_log  = T
+                            , log_value = log10
+                            , my_logo_col = 'hydrophobicity'
+                            #, theme_bgc
+                            # , xfont_bgc 
+                            # , yfont_bgc 
+                            , 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 = 25 # title size
+                            , y_tts = 20
+                            , leg_pos = "none"
+                            , leg_ts = 15 # leg text size
+                            , leg_tts = 16 # leg title size
+)