R/get_boxplot_colors.R

In kuppal2/xmsPANDA: R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

get_boxplot_colors <-
function(boxplot.col.opt,class_labels_levels){
  
  alphacol=0.4
  
  if(is.na(boxplot.col.opt)==TRUE){
    
    col_vec<-rep(c("white"),length(class_labels_levels))
    boxplot.col.opt<-col_vec
  }
  
  if(boxplot.col.opt=="default"){
    
    col_vec<-c("#CC0000","#AAC000","blue","mediumpurple4","mediumpurple1","blueviolet","cornflowerblue","cyan4","skyblue",
               "darkgreen", "seagreen1", "green","yellow","orange","pink", "coral1", "palevioletred2",
               "red","saddlebrown","brown","brown3","white","darkgray","aliceblue",
               "aquamarine","aquamarine3","bisque","burlywood1","lavender","khaki3","black")
    
  }else{
    if(boxplot.col.opt=="topo"){
      #col_vec<-topo.colors(256) #length(class_labels_levels))
      
      #col_vec<-col_vec[seq(1,length(col_vec),)]
      
      col_vec <- topo.colors(length(class_labels_levels), alpha=alphacol)
    }else{
      if(boxplot.col.opt=="heat"){
        #col_vec<-heat.colors(256) #length(class_labels_levels))
        
        col_vec <- heat.colors(length(class_labels_levels), alpha=alphacol)
      }else{
        if(boxplot.col.opt=="rainbow"){
          #col_vec<-heat.colors(256) #length(class_labels_levels))
          col_vec<-rainbow(length(class_labels_levels), start = 0, end = alphacol)
          
          #col_vec <- heat.colors(length(class_labels_levels), alpha=alphacol)
        }else{
          
          if(boxplot.col.opt=="terrain"){
            #col_vec<-heat.colors(256) #length(class_labels_levels))
            #col_vec<-rainbow(length(class_labels_levels), start = 0, end = alphacol)
            
            col_vec <- cm.colors(length(class_labels_levels), alpha=alphacol)
          }else{
            
            if(boxplot.col.opt=="colorblind"){
              #col_vec <-c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")
              # col_vec <- c("#0072B2", "#E69F00", "#009E73", "gold1", "#56B4E9", "#D55E00", "#CC79A7","black")
              
              if(length(class_labels_levels)<9){
                
                col_vec <- c("#0072B2", "#E69F00", "#009E73", "#56B4E9", "#D55E00", "#CC79A7", "#E64B35FF", "grey57")
                
              }else{
                
                #   col_vec<-colorRampPalette(brewer.pal(10, "RdBu"))(length(class_labels_levels))
                col_vec<-c("#0072B2", "#E69F00", "#009E73", "#56B4E9", "#D55E00", "#CC79A7","#E64B35B2", "#4DBBD5B2","#00A087B2","#3C5488B2","#F39B7FB2","#8491B4B2","#91D1C2B2","#DC0000B2","#7E6148B2",
                           "#374E55B2","#DF8F44B2","#00A1D5B2","#B24745B2","#79AF97B2","#6A6599B2","#80796BB2","#0073C2B2","#EFC000B2", "#868686B2","#CD534CB2","#7AA6DCB2","#003C67B2","grey57")
                
              }
              
              
            }else{
              
              check_brewer<-grep(pattern="brewer",x=boxplot.col.opt)
              
              if(length(check_brewer)>0){
                
                boxplot.col.opt=gsub(x=boxplot.col.opt,pattern="brewer.",replacement="")
                col_vec <- colorRampPalette(brewer.pal(10, boxplot.col.opt))(length(class_labels_levels))
                
              }else{
                
                if(boxplot.col.opt=="journal"){
                  
                  
                  col_vec<-c("#0072B2", "#E69F00", "#009E73", "#56B4E9", "#D55E00", "#CC79A7","#E64B35FF","#3C5488FF","#F39B7FFF",
                             "#8491B4FF","#91D1C2FF","#DC0000FF","#B09C85FF","#5F559BFF",
                             "#808180FF","#20854EFF","#FFDC91FF","#B24745FF",
                             
                             "#374E55FF","#8F7700FF","#5050FFFF","#6BD76BFF",
                             "#E64B3519","#4DBBD519","#631879E5","grey75")
                  if(length(class_labels_levels)<8){
                    col_vec<-c("#0072B2", "#E69F00", "#009E73", "#56B4E9", "#D55E00", "#CC79A7","grey75")
                    
                    #col_vec2<-brewer.pal(n = 8, name = "Dark2")
                    
                  }else{
                    if(length(class_labels_levels)<=28){
                      # col_vec<-c("#0072B2", "#E69F00", "#009E73", "#56B4E9", "#D55E00", "#CC79A7", "grey75","#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02", "#A6761D", "#666666","#1B9E77", "#7570B3", "#E7298A", "#A6761D", "#666666", "#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02", "#A6761D", "#666666")
                      
                      col_vec<-c("#0072B2", "#E69F00", "#009E73", "#56B4E9", "#D55E00", "#CC79A7","#E64B35FF","#3C5488FF","#F39B7FFF",
                                 "#8491B4FF","#91D1C2FF","#DC0000FF","#B09C85FF","#5F559BFF",
                                 "#808180FF","#20854EFF","#FFDC91FF","#B24745FF",
                                 
                                 "#374E55FF","#8F7700FF","#5050FFFF","#6BD76BFF", "#8BD76BFF",
                                 "#E64B3519","#9DBBD0FF","#631879E5","#666666","grey75")
                      
                    }else{
                      
                      
                      
                      
                      colfunc <-colorRampPalette(c("#0072B2", "#E69F00", "#009E73", "#56B4E9", "#D55E00", "#CC79A7","grey75"));col_vec<-colfunc(length(class_labels_levels))
                      
                      col_vec<-col_vec[sample(col_vec)]
                      
                      
                    }
                  }
                  
                  
                  
                }else{
                  col_vec <-boxplot.col.opt
                }
                
              }
              
            }
          }
          
          
        }
        
      }
      
    }
  }
  
  return(col_vec)
  
}