fun/fun-protlines.R

In marcottelab/pepliner: MS Data Visualization

protlineplot_dat <- function(df_norm_prot, ids, protsel_id){
   print("protlines_dat")
   df_sel <- df_norm_prot %>% filter(ID %in% protsel_id)
   #print(names(df_sel))
   return(df_sel)
}

protlineplot_fun <- function(df_norm_prot, 
                             ids,
                             protsel_id,
                             yaxis="ProteinCount",
                             fill="#E69F00FF",
                             size = 0.3,
                             scale = 0.9,
                             min_graphic_details = FALSE,
                             condition = FALSE,
                             facets = NULL,
                             protnormscale = "Protein",
                             protnormgroup = "Experiment",
                             condition_palette=c("red", "black", "lightblue", "orange")
                             )
{
   print("lines_fun")
   #print(names(df_norm_prot))
   #print(protsel_id)
   df_sel <- df_norm_prot %>% filter(ID %in% protsel_id)
   
   print(head(df_sel))

   if(protnormscale ==  "None"){
      protlines <- ggplot(data = df_sel, aes(x = FractionID, y = ID, height = ProteinCount)) #, fill=Condition)) +
   }

   if(protnormscale ==  "Protein" && protnormgroup == "Experiment"){
      protlines <- ggplot(data = df_sel, aes(x = FractionID, y = ID, height = ExpNormProteinCount)) #, fill=Condition)) +
   }

   if(protnormscale ==  "Protein" && protnormgroup == "None"){
      protlines <- ggplot(data = df_sel, aes(x = FractionID, y = ID, height = ProtNormProteinCount)) #, fill=Condition)) +
   } 




    protlines <- protlines + 
    theme(
    strip.background = element_blank(),
    strip.text = element_text(face = "bold", size=8, margin = margin(0)),
    axis.text.x= element_blank(),
    axis.title.x = element_blank(),
    axis.title.y = element_blank(),
    axis.line.x = element_blank(),
    axis.line.y = element_blank(),
    axis.ticks.x = element_blank(),
    axis.ticks.y = element_blank()#,
    #legend.position = "none"
    ) 

  if(condition == TRUE){
      protlines <- protlines + geom_ridgeline(stat = "identity", scale = scale, size = size, alpha = 0, aes(color = condition, group=paste(condition, ID))) +
                                                        scale_color_manual(values = condition_palette) 
  }
  else{
      protlines <- protlines + geom_ridgeline(stat = "identity", scale = scale, fill = fill, size = size, aes(group=ID)) 
  }


  #protlines <- protlines + facet_wrap(~ExperimentID)
  #ggsave(filename = "TEST.png", protlines, device = "png")

  if(!is.null(facets)){
  
      facet_str <- paste(facets, collapse = ' + ')
      facet_str <- paste("~", facet_str, sep="")
      #Final construct needs to be ~A + B + C + D.
      #If only one facet variable, will get  ~A
      print(facet_str)
      print(names(df_sel)) 
     #Facet_grid takes a string. Facet_wrap does not. 
      protlines <- protlines + facet_grid(facet_str, scales = "free_x") 
      #browser()
      #protlines <- protlines + facet_wrap(~ExperimentID) #, scales = "free_x") 
      #browser()
      print("HERE")
  } 

  if(min_graphic_details == TRUE){
      protlines <- protlines + theme_nothing()
 
  }



  #g <- ggplotly(lines)
  #ggsave(cov, filename = "testing.png")
  return(protlines)
  #g <- ggplotly()
  #htmlwidgets::saveWidget(g, "test.html")
  #return(g)
  #g %>% layout()   
  
}