lf_bp2

scripts/Header_TT.R

@@ -236,6 +236,19 @@ consurf_colours = c(#"0" = rgb(1.00,1.00,0.59)
                     , "9" = rgb(0.04,0.49,0.51)
                     )
 
+consurf_bp_colours = c(#"0" = rgb(1.00,1.00,0.59)
+    "0" = rgb(1.00,1.00,0.59)
+  , "1" = rgb(0.63,0.16,0.37)
+  , "2" = rgb(0.94,0.49,0.67)
+  , "3" = rgb(0.98,0.78,0.86)
+  , "4" = rgb(0.98,0.92,0.96)
+  , "5" = rgb(1.00,1.00,1.00)
+  , "6" = rgb(0.84,0.94,0.94)
+  , "7" = rgb(0.65,0.86,0.90)
+  , "8" = rgb(0.29,0.69,0.75)
+  , "9" = rgb(0.04,0.49,0.51)
+)
+
 ##################################################
 
 # Function name clashes with plyr and dplyr

scripts/functions/lf_bp.R

@@ -28,7 +28,8 @@ lf_bp <- function(lf_df = lf_duet
                   , stat_grp_comp = c("R", "S")
                   , stat_method = "wilcox.test"
                   , my_paired = FALSE
-                  , stat_label = c("p.format", "p.signif") ){
+                  , stat_label = c("p.format", "p.signif")
+                  ) {
   
   fwv = as.formula(paste0("~", facet_var))
   #fwv = reformulate(facet_var)
@@ -57,13 +58,22 @@ lf_bp <- function(lf_df = lf_duet
                   , outlier.colour = NA
                   #, position = position_dodge(width = 0.9)
                   , width = bp_width) + 
-      geom_quasirandom(priority = "density"
+      geom_quasirandom(#priority = "density"
                     #, shape = 21
-                    , size = dot_size
+                    size = dot_size
                     , alpha = dot_transparency
                     , show.legend = FALSE
                     , cex = 0.8
-                    , aes(colour = factor(eval(parse(text = colour_categ))) ))  
+                    , aes(
+                      colour = factor(
+                        eval(
+                          parse(
+                            text = colour_categ
+                            )
+                          )
+                        )
+                      )
+                    ) + ggplot2::scale_color_manual(values = consurf_bp_colours)  
       
     } else {
     #Legend=factor(eval(parse(text = colour_categ)))
@@ -71,16 +81,26 @@ lf_bp <- function(lf_df = lf_duet
     p2 = p1 +
       #theme(legend.title=element_text('XXX')) + # Legend doesn't need a title)
       
-      geom_quasirandom(priority = "density"
+      geom_quasirandom(#priority = "density"
                     #, shape = 21
-                    , size = dot_size
+                    size = dot_size
                     , alpha = dot_transparency
                     , show.legend = FALSE
                     # , fast = FALSE
                     , cex = 0.8
-                    , aes(colour = factor(eval(parse(text = colour_categ))) )
+                    , aes(
+                      colour = factor(
+                        eval(
+                          parse(
+                            text = colour_categ
+                            )
+                          )
+                        )
+                      )
                     #, aes(colour = Legend)
-                    )
+                    ) +
+      ggplot2::scale_color_manual(values = consurf_bp_colours)
+
 
     }
 
@@ -115,6 +135,7 @@ lf_bp <- function(lf_df = lf_duet
                        , method = stat_method
                        , paired = my_paired
                        , label = stat_label[2])
+      
     return(OutPlot)
     }
    

scripts/functions/lf_bp2.R

@@ -0,0 +1,147 @@
+#############################
+# Barplots: ggplot
+# stats +/-
+# violin +/-
+# barplot +/
+# beeswarm
+#############################
+
+lf_bp2 <- function(lf_df = lf_duet
+                   , p_title = "DUET-DDG"
+                   , colour_categ = "outcome"
+                   , x_grp = "mutation_info_labels"
+                   , y_var = "param_value"
+                   , facet_var = "param_type"
+                   , n_facet_row = 1
+                   , y_scales = "free_y"
+                   , colour_bp_strip = "khaki2"
+                   , dot_size = 3
+                   , dot_transparency = 0.5
+                   , violin_quantiles = c(0.25, 0.5, 0.75) # can be NULL
+                   , my_ats = 22 # axis text size
+                   , my_als = 20 # axis label size
+                   , my_fls = 20 # facet label size
+                   , my_pts = 22 # plot title size)
+                   , make_boxplot = FALSE
+                   #, bp_width = c("auto", 0.5)
+                   , bp_width = "auto"
+                   , add_stats = TRUE
+                   , stat_grp_comp = c("R", "S")
+                   , stat_method = "wilcox.test"
+                   , my_paired = FALSE
+                   , stat_label = c("p.format", "p.signif")
+                   , monochrome = FALSE
+) {
+  
+  fwv = as.formula(paste0("~", facet_var))
+  #fwv = reformulate(facet_var)
+  
+  # Only use the longer colour palette if there are many outcomes
+  if (length(levels(lf_df$outcome)) > 2) {
+    lf_bp_colours = consurf_bp_colours  
+  }
+  else {
+    lf_bp_colours =NULL
+    #lf_bp_colours = hue_pal()(2)
+    
+  }
+  
+  
+  if (bp_width == "auto"){
+    bp_width = 0.5/length(unique(lf_df[[x_grp]]))
+  }else{
+    bp_width = bp_width
+  }
+  
+  ggplot(lf_df, aes_string(x = x_grp, y = y_var))  +
+    
+    
+    facet_wrap(fwv
+               , nrow = n_facet_row
+               , scales = y_scales) +
+    
+    ggplot2::scale_color_manual(values = lf_bp_colours) +
+    
+    geom_violin(trim = T
+                , scale = "width"
+                #, position = position_dodge(width = 0.9)
+                , draw_quantiles = violin_quantiles) +
+    
+    # Add formatting to graph
+    theme(axis.text.x = element_text(size = my_ats)
+          , axis.text.y = element_text(size = my_ats
+                                       , angle = 0
+                                       , hjust = 1
+                                       , vjust = 0)
+          , axis.title.x = element_text(size = my_ats)
+          , axis.title.y = element_text(size = my_ats)
+          , plot.title = element_text(size = my_pts
+                                      , hjust = 0.5
+                                      , colour = "black"
+                                      , face = "bold")
+          , strip.background = element_rect(fill = colour_bp_strip)
+          , strip.text.x = element_text(size = my_fls
+                                        , colour = "black")
+          , legend.title = element_text(color = "black"
+                                        , size = my_als)
+          , legend.text = element_text(size = my_ats)
+          , legend.direction = "vertical") +
+    
+    labs(title = p_title
+         , x = ""
+         , y = "") +
+    
+    if (add_stats){
+      my_comparisonsL <- list( stat_grp_comp )
+      
+      stat_compare_means(comparisons = my_comparisonsL
+                         , method = stat_method
+                         , paired = my_paired
+                         , label = stat_label[2])
+      
+      
+      if (make_boxplot){
+        geom_boxplot(fill = "white"
+                     , outlier.colour = NA
+                     #, position = position_dodge(width = 0.9)
+                     , width = bp_width) + 
+          
+          geom_quasirandom(#priority = "density"
+            #, shape = 21
+            size = dot_size
+            , alpha = dot_transparency
+            , show.legend = FALSE
+            , cex = 0.8
+            , aes(
+              colour = factor(
+                eval(
+                  parse(
+                    text = colour_categ
+                  )
+                )
+              )
+            )
+          )
+        
+      } else {
+        geom_quasirandom(
+          size = dot_size
+          , alpha = dot_transparency
+          , show.legend = FALSE
+          # , fast = FALSE
+          , cex = 0.8
+          , aes(
+            colour = factor(
+              eval(
+                parse(
+                  text = colour_categ
+                )
+              )
+            )
+          )
+        )
+      }
+    }
+}
+
+#lf_bp2(lf_consurf)

scripts/functions/logoP_or.R

@@ -110,15 +110,15 @@ LogoPlotCustomH <- function(plot_df
     
   }
   
-  class(logo_dfP_wf)
+  #class(logo_dfP_wf)
   
   rownames(logo_dfP_wf) = logo_dfP_wf[,1]
-  dim(logo_dfP_wf)
+  #dim(logo_dfP_wf)
   
   logo_dfP_wf = logo_dfP_wf[,-1]
-  str(logo_dfP_wf)
+  #str(logo_dfP_wf)
   
-  colnames(logo_dfP_wf)
+  #colnames(logo_dfP_wf)
   position_or = as.numeric(colnames(logo_dfP_wf))
   
   ######################################