R/rotate_dot_plot_dendrogram.R

In Simon-Leonard/FlexDotPlot: Flexible Dot Plot

#' Interactively rotate dendrograms from dot_plot outputs
#'
#' Take a output from dot_plot function and allow interactive dendrogram rotation with dendextend package
#'
#' @encoding UTF-8
#' @param dot_plot_output Output from \code{\link{dot_plot}} function function
#' @param axis_to_rotate Dendrogram to rotate "x" or "y"
#'
#' @import ggplot2
#' @importFrom dendextend click_rotate labels<-
#'
#' @return Print and return rotated dot plot
#' @export
#' @examples
#' # Perform dot_plot
#' if(interactive()){
#' library(FlexDotPlot)
#' data(CBMC8K_example_data)
#'
#' # Run dot_plot
#' dotplot_output = dot_plot(data.to.plot=CBMC8K_example_data, size_var="RNA.avg.exp.scaled",
#' dend_x_var=c("RNA.avg.exp.scaled","ADT.avg.exp.scaled"),
#' dend_y_var=c("RNA.avg.exp.scaled","ADT.avg.exp.scaled"),
#' dist_method="euclidean",hclust_method="ward.D", do.return = TRUE)
#'
#' # The following command has to be run when the user
#' #is running example("rotate_dot_plot_dendrogram") only.
#' dotplot_output$command=call("dot_plot", data.to.plot=as.name("CBMC8K_example_data"),
#' size_var="RNA.avg.exp.scaled",
#' dend_x_var=c("RNA.avg.exp.scaled","ADT.avg.exp.scaled"),
#' dend_y_var=c("RNA.avg.exp.scaled","ADT.avg.exp.scaled"),
#' dist_method="euclidean",hclust_method="ward.D", do.return = TRUE)
#'
#' # y  dendrogram rotation
#' r1=rotate_dot_plot_dendrogram(dotplot_output, axis_to_rotate = "y")
#' # add x dendrogram rotation to previous result
#' #r2=rotate_dot_plot_dendrogram(r1, axis_to_rotate = "x")
#' }
#' @author Simon Leonard - simon.leonard@univ-rennes1.fr

rotate_dot_plot_dendrogram=function(dot_plot_output, axis_to_rotate=c("x","y")){

  axis_to_rotate=match.arg(axis_to_rotate)


  ### Check that dot_plot_output is an output of dot_plot_function ----
  if(class(dot_plot_output)!="list"){
    stop("input object not supported, please provide an output from the dot_plot function")
  }
  if(!all(c("input_data","command","plot") %in% names(dot_plot_output))){
    stop("input object not supported, please provide an output from the dot_plot function")
  }

  # Check that dendrogram were computed
  if(axis_to_rotate=="x" & (!"dendrogram_x" %in% names(dot_plot_output))){
    stop("Cannot rotate x dendrogramm as it was not computed")
  }
  if(axis_to_rotate=="y" & (!"dendrogram_y" %in% names(dot_plot_output))){
    stop("Cannot rotate y dendrogramm as it was not computed")
  }



  ### Rotate dendrogram and change levels order ----
  index=ifelse(axis_to_rotate=="x",1,2)

  dend_to_rotate=dot_plot_output[[paste("dendrogram", axis_to_rotate, sep="_")]]
  labels(dend_to_rotate)=levels(dot_plot_output$input_data[,index])

  new_dend=click_rotate(dend_to_rotate, continue = TRUE)

  dot_plot_output$input_data[,index]=factor(dot_plot_output$input_data[,index], levels=labels(new_dend))



  ### Performing dotplot again without dendrogramms----
  # Get original command & modify some parameters (no plot no original dendro)
  print(names(dot_plot_output))
  com=dot_plot_output$command
  print(com)
  print(names(com))
  com[[paste("dend",axis_to_rotate,"var", sep="_")]]=NULL
  com$do.plot=FALSE

  # Replace data.to.plot input with the re ordered one
  com=as.character(as.expression(com))
  com=gsub("\n","",com)

  part1=gregexpr("dot_plot\\(", com)[[1]][1]
  part1_end=part1+nchar("dot_plot(")

  part2=gregexpr(",", com)[[1]][1]

  com=paste(substring(com, part1, part1_end-1),
       "dot_plot_output$input_data",
       substring(com, part2), sep="")

  # Execute new dot plot
  new_dot_plot=eval(parse(text = com))



  ### Adding dendrogram to new dotplot plot and output object ----
  new_dot_plot[[paste("dendrogram", axis_to_rotate, sep="_")]]=new_dend
  new_dend_data=segment(dendro_data(new_dend))

  if(axis_to_rotate=="y"){

    dendro_vertical <- dot_plot_output$raw_dend_ggplot + geom_segment(data = new_dend_data, mapping = aes_(x=~length(labels(dend_to_rotate))+0.5-y,
                                                                          xend=~length(labels(dend_to_rotate))+0.5-yend,
                                                                          y=~x,yend=~xend, label=NULL))
    # dendro_vertical <- dendro_vertical+ theme_void() +
    #   coord_cartesian(xlim = range(c(length(labels(dend_to_rotate))+0.5-new_dend_data$y,length(labels(dend_to_rotate))+0.5-new_dend_data$yend)),
    #                                                    ylim=c(0.5,length(labels(dend_to_rotate))+0.5),
    #                                                    expand=F, default = T) + theme(plot.margin = unit(c(0,0,0,2), units = "points"))
    # dendro_vertical <- dendro_vertical+ theme_void()

    new_dot_plot$plot[[1]][[3]]=dendro_vertical

    #Keep other dendrogram from input object
    new_dot_plot$plot[[1]][[1]]=dot_plot_output$plot[[1]][[1]]

  }else{
    dendro_horizontal <- dot_plot_output$raw_dend_ggplot + geom_segment(data = new_dend_data, mapping = aes_(x=~x,xend=~xend,
                                                                            y=~y,yend=~yend, label=NULL))
    dendro_horizontal <- dendro_horizontal+ theme_void()

    new_dot_plot$plot[[1]][[1]]=dendro_horizontal

    #Keep other dendrogram from input object
    new_dot_plot$plot[[1]][[3]]=dot_plot_output$plot[[1]][[3]]
  }


  ### final output ----
  # Arrange final object
  layout=rbind(c(NA,NA,1,NA,NA,NA,NA),
               c(NA,NA,2,NA,NA,NA,NA),
               c(3,4,5,6,7,8,9),
               c(NA,NA,10,NA,NA,NA,NA))
  final_plot=grid.arrange(grobs=new_dot_plot$plot[[1]],
                         layout_matrix = layout,
                         widths =dot_plot_output$plot$widths,
                         heights = dot_plot_output$plot$heights)
  new_dot_plot$plot=final_plot

  # Add dot plot command to object
  new_dot_plot$command=parse(text=com)[[1]]

  #Return object
  return(new_dot_plot)

}