added the scratch script as _v2 to play while repurposing bp_subcolours.R

2021-09-15 19:34:24 +01:00 · 2021-09-15 19:34:24 +01:00 · 6d542e7634
commit 6d542e7634
parent 1f19c26c2d
1 changed files with 104 additions and 0 deletions
--- a/scripts/functions/redundant/bp_subcolours_v2.R
+++ b/scripts/functions/redundant/bp_subcolours_v2.R
@ -0,0 +1,104 @@
+#########################################################
+# 1b: Define function: coloured barplot by subgroup
+# LINK: https://stackoverflow.com/questions/49818271/stacked-barplot-with-colour-gradients-for-each-bar
+#########################################################
+
+ColourPalleteMulti = function(df, group, subgroup){
+  
+  # Find how many colour categories to create and the number of colours in each
+  categories <- aggregate(as.formula(paste(subgroup, group, sep="~" ))
+                          , df
+                          , function(x) length(unique(x)))
+  #  return(categories) }
+  
+  category.start <- (scales::hue_pal(l = 100)(nrow(categories))) # Set the top of the colour pallete
+  
+  category.end  <- (scales::hue_pal(l = 40)(nrow(categories))) # set the bottom
+  
+  #return(category.start); return(category.end)}
+  
+  # Build Colour pallette
+  colours <- unlist(lapply(1:nrow(categories),
+                           function(i){
+                             colorRampPalette(colors = c(category.start[i]
+                                                         , category.end[i]))(categories[i,2])}))
+  return(colours)
+}
+#########################################################################
+
+bp_stability_hmap <- function(plotdf = merged_df3
+                              , xvar_colname = "position"
+                              #, bar_col_colname = "group"
+                              , stability_colname = "duet_scaled"
+                              , stability_outcome_colname = "duet_outcome"
+                              , p_title = ""  # "Protein stability (DUET)"
+                              , my_xaxls = 12 # x-axis label size
+                              , my_yaxls = 20 # y-axis label size
+                              , my_xaxts = 18 # x-axis text size
+                              , my_yaxts = 20 # y-axis text size
+                              , my_pts  = 20  # plot-title size
+                              , my_xlab = "Position"
+                              , my_ylab = "No. of nsSNPs"
+                              )
+{
+
+  # order the df by position and ensure it is a factor
+  plotdf = plotdf[order(plotdf[[xvar_colname]]), ]
+  plotdf[[xvar_colname]] = factor(plotdf[[xvar_colname]])
+  
+  #cat("\nSneak peak:\n")
+  head(data.frame( plotdf[[xvar_colname]], plotdf[[stability_colname]] ) )
+
+  # stability values isolated to help with generating column called: 'group'
+  my_grp = plotdf[[stability_colname]]
+  cat( "\nLength of nsSNPs:", length(my_grp)
+       , "\nLength of unique values for nsSNPs:", length(unique(my_grp)) )
+  
+  # Add col: 'group'
+  plotdf$group = paste0(plotdf[[stability_outcome_colname]], "_", my_grp, sep = "")
+
+  # check unique values in normalised data
+  cat("\nNo. of unique values in", stability_colname, "no rounding:"
+      , length(unique(plotdf[[stability_colname]])))
+  
+  # Call the function to create the palette based on the group defined above
+  #subcols_ps
+  subcols_bp_hmap = ColourPalleteMulti(plotdf, stability_outcome_colname, stability_colname)
+  
+  cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
+  
+  #-------------------------------
+  # Generate the subcols barplot
+  #-------------------------------
+  
+  #g = ggplot(plotdf, aes(x = factor(position, ordered = T)))
+  g = ggplot(plotdf, aes_string(x = xvar_colname
+                               # , ordered = T)
+             ))
+  
+
+  OutWidePlot = g + geom_bar(aes(fill = group)
+                             , colour = "grey") +
+    
+  scale_fill_manual( values = subcols_bp_hmap
+                       , guide = "none") +
+    
+    theme( axis.text.x = element_text(size = my_xaxls
+                                      , angle = 90
+                                      , hjust = 1
+                                      , vjust = 0.4)
+           , axis.text.y = element_text(size = my_yaxls
+                                        , angle = 0
+                                        , hjust = 1
+                                        , vjust = 0)
+           , axis.title.x = element_text(size = my_xaxts)
+           , axis.title.y = element_text(size = my_yaxts ) 
+           , plot.title = element_text(size = my_pts
+                                       , hjust = 0.5)) +
+    
+    labs(title = p_title
+         , x = my_xlab
+         , y = my_ylab)
+
+  return(OutWidePlot)
+}