lbe3df: 3D Fluorescence spectra processing

#' 3D Fluorescence level plot by plotly, after processing
#'
#' After running LBE_fluo3D_processing() with your options, run this function to visualize and export your surface plot. Results (plots in pdf and/or png and/or interactive html) will be exported to a folder inside your directory called "Output_data".
#' @param x The default value of "x_vector" is assuming that "LBE_fluo3D_processing" have just been used. Otherwise it must be a vector containing the emission wavelenghts range.
#' @param y The default value of "y_vector" is assuming that "LBE_fluo3D_processing" have just been used. Otherwise it must be a vector containing the excitation wavelenghts range.
#' @param z The default value of "xy_vector" is assuming that "LBE_fluo3D_processing" have just been used. Otherwise you must provide a matrix containing the z values (intensity) where X must be the lines, Y must be the columns and Z must be the values of the table.
#' @param plot_zones_polygons Boolean (TRUE or FALSE). It allows you to chose wether you want to plot the polygons with the 7 zones or not.
#' @param export_html TRUE or FALSE. It allows you to chose wether you want to export a plotly html interactive file (might generate about 3 MB).
#' @param export_png TRUE or FALSE. It allows you to chose wether you want to export a png static plot.
#' @param export_pdf TRUE or FALSE. It allows you to chose wether you want to export a png static plot.
#' @param n_color Number of colors that will be picked up in the color palette to build the color scale. Normally it is relevant only for color scales containing several colors.
#' @param color_palette 1 to 9. Default is 1 for "viridis" (optimized for all types color blindness and with no loss of information for black and white printing). Use 2 for "gray.colors" if you want directly a black and white plot. You can select other interesting color scales such magma (3), plasma (4), inferno (5), terrain.colors (6),topo.colors (7), cm.colors (8) and matlab.like2 (9). The last one is the same used in the references in the website of the International Humic Substances Society (2018).
#' @param directory Default is the working directory. Better not change it.
#' @param sample_name_ Default is the output from processing function. Better not change it.
#' @param zones_polygons_ Default corresponds to the 7 zones defined in Jimenez et. al 2015. Otherwise, you must provide a data frame object containing three columns: one "id" column where you identify your zones for each xy coordinate. one "x" column where you put all the x coordinates (emission wavelenght). one "y" column where you put evey y coordinate (excitation wavelenght). The points of a polygon must be ordered in a way that the polygon is "closed" and must include repete the first point as a final point.
#' @keywords 3D fluorescence
#' @export
#' @examples
#' > setwd(XXXX) #XXX is your directory contaning the .sp files (copy and paste from the brownse and replace all the "\" by "/").
#' > LBE_fluo3D_processing() #include your options if you want.
#' > LBE_fluo3D_levelplot(color_palette="gray.colors") #export pdf and png with a black and white surface plot.

LBE_fluo3D_levelplot=function(x=x_vector, #assuming that "LBE_fluo3D_processing" have just been used
                              y=y_vector,  #assuming that "LBE_fluo3D_processing" have just been used
                              z=xy_vector,  #assuming that "LBE_fluo3D_processing" have just been used
                              plot_zones_polygons=TRUE,
                              export_html=FALSE,
                              export_png=TRUE,
                              export_pdf=TRUE,
                              n_color=10,
                              color_palette=1,
                              directory=directory_processing,
                              sample_name_=sample_name,
                              zones_polygons_="Default"
                              ) {

  #print(1)
  print("Setting directories")
  wd_out=paste0(directory,"/Output_data")
  dir.create(wd_out)

  #### 1.2 Definition of 3DF' zones ####
  #### 1.2.1 3DF Zone, polygons coordinates ####
  print("Defining polygons")
  if (plot_zones_polygons) {

    list_polygons=zones_definition(zones_polygons_)

    #### 1.2.2 3DF Zones, text coordinates ####
    for (i in 1:length(table(list_polygons[,1]))) {
      print(i)
    zone_id=names(table(list_polygons[,1]))[i]
    text_zone_i=data.frame(id=zone_id,
                            x=(mean(list_polygons$x[which(list_polygons$id==zone_id)])),
                            y=(mean(list_polygons$y[which(list_polygons$id==zone_id)])))
    assign(paste0("text_zone",i),text_zone_i)
    if (i==1) {list_text_zones=text_zone1}else {list_text_zones=rbind(list_text_zones,text_zone_i)}}

  } else {
    list_polygons=data.frame(id="",x=c(201,201),y=c(201,201))  #just empty
    list_text_zones=data.frame(id="",x=350,y=350)              #just empty
  }

print("Working on plots")
  n_color=n_color
list_colorfunction=list(viridis,gray.colors,magma,plasma,inferno,terrain.colors,topo.colors,cm.colors,matlab.like2)
colorfunction=list_colorfunction[[color_palette]]
#print(4)
  print(plot_ly(x=as.numeric(x),
                y=as.numeric(y),
                z=t(as.matrix(z)),
                type="contour",
                #coloring="heatmap",
                colorscale = data.frame(seq(0,1,length.out=n_color),colorfunction(n_color))) %>%  #instead of viridis, other pallete can be used such as magma, plasma, inferno
          layout(                        # all of layout's properties: /r/reference/#layout
            title = "3D fluorescence spectrum", # layout's title: /r/reference/#layout-title
            xaxis = list(           # layout's xaxis is a named list. List of valid keys: /r/reference/#layout-xaxis
              title = "Emission",      # xaxis's title: /r/reference/#layout-xaxis-title
              showgrid = T),       # xaxis's showgrid: /r/reference/#layout-xaxis-showgrid
            yaxis = list(           # layout's yaxis is a named list. List of valid keys: /r/reference/#layout-yaxis
              title = "Excitation")) %>%  # yaxis's title: /r/reference/#layout-yaxis-title
          add_polygons(z=NULL,
                       colorscale=NULL,
                       x=list_polygons$x,
                       y=list_polygons$y,
                       split=list_polygons$id,
                       line=list(color="black",width=2),
                       opacity=1,
                       fillcolor='rgba(7, 164, 181, 0)',  ##only way to keep lines black with no fill was to set a color with tgis rgba funtion with 4th digit of 0
                       showlegend=T) %>%
          add_annotations(z=NULL,
                          colorscale=NULL,
                          x=list_text_zones$x,
                          y=list_text_zones$y,
                          text=list_text_zones$id,
                          split=list_text_zones$id,
                          showlegend=F,
                          showarrow=F,
                          font=list(color="white",size=20)))

  print("Exporting plots")

  if (export_html) {
    htmlwidgets::saveWidget(as_widget(last_plot()), paste0(wd_out,"/",sample_name_,"_contour_plot.html"))}

  if (export_pdf){
  plotly_exp_directory_pdf=paste0(wd_out,"/",sample_name_,"_contour_plot.pdf")
  export(p=last_plot(),file=plotly_exp_directory_pdf)
  }

  if (export_png){
  plotly_exp_directory_png=paste0(wd_out,"/",sample_name_,"_contour_plot.png")
  export(p=last_plot(),file=plotly_exp_directory_png)
  }
} #end of the function