R/genCircularStatic.R

In chenh2017/parsenetwork: The Network for PARSE HEALTH

#' @importFrom dplyr %>% left_join
#' @import ggplot2
#' @importFrom rlang .data
#' @importFrom graphics title
#' @importFrom stats end na.omit start

## Generate circular plot using ggplot =======================================
circularPreData <- function(data){
  # Set a number of 'empty bar' to add at the end of each group
  empty_bar=3
  to_add = data.frame( matrix(NA, empty_bar*nlevels(data$group), ncol(data)) )
  colnames(to_add) = colnames(data)
  to_add$group=rep(levels(data$group), each=empty_bar)
  data=rbind(data, to_add)
  data=data %>% dplyr::arrange(.data$group)
  data$id=seq(1, nrow(data))
  
  # Get the name and the y position of each label
  label_data=data
  number_of_bar=nrow(label_data)
  angle= 90 - 360 * (label_data$id-0.5) /number_of_bar     # I substract 0.5 because the letter must have the angle of the center of the bars. Not extreme right(1) or extreme left (0)
  label_data$hjust<-ifelse( angle < -90, 1, 0)
  label_data$angle<-ifelse(angle < -90, angle+180, angle)
  
  # prepare a data frame for base lines
  base_data=data %>%
    dplyr::group_by(.data$group) %>%
    dplyr::summarize(start=min(.data$id), end=max(.data$id) - empty_bar) %>%
    dplyr::rowwise() %>%
    dplyr::mutate(title=mean(c(.data$start, .data$end)))
  
  
  # prepare a data frame for grid (scales)
  grid_data = base_data
  grid_data$end = grid_data$end[c( nrow(grid_data), 1:nrow(grid_data)-1)] + 1
  grid_data$start = grid_data$start - 1
  if(nrow(grid_data)>1){
    grid_data=grid_data[-1,]
  }else{
    grid_data$start = -1
  }
  return(list(`data` = data, `label_data` = label_data, 
              `grid_data` = grid_data, `base_data` = base_data))
}

circularStatic <- function(df_edges, 
                           dict.combine, 
                           ColorsCirc){
  
      nodes = df_edges$to
      data = data.frame(
        "individual"=dict.combine$term[match(nodes,dict.combine$id)],
        "group"=dict.combine$group1[match(nodes,dict.combine$id)],
        "type" = dict.combine$type[match(nodes,dict.combine$id)],
        "value"=df_edges$cos
      )
      data = data %>% dplyr::arrange(.data$type, .data$group, .data$value)
      if(nrow(data)>0){
        data$value = data$value*100
        data$group = factor(data$group)
        
        circularData = circularPreData(data)
        data = circularData$data
        label_data = circularData$label_data
        grid_data = circularData$grid_data
        base_data = circularData$base_data
        
        # Make the plot
        p = ggplot(data, aes(x=as.factor(.data$id), y=.data$value, fill=match(.data$group, ColorsCirc$group))) +       # Note that id is a factor. If x is numeric, there is some space between the first bar
          scale_fill_manual(values = ColorsCirc$color) +
          geom_bar(aes(x=as.factor(.data$id), y=.data$value, fill=.data$group), stat="identity", alpha=0.5) +
          
          # Add a val=.8/.6/.4/.2 lines. I do it at the beginning to make sur barplots are OVER it.
          geom_segment(data=grid_data, aes(x = .data$end, y = 80, xend = start, yend = 80), colour = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
          geom_segment(data=grid_data, aes(x = .data$end, y = 60, xend = start, yend = 60), colour = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
          geom_segment(data=grid_data, aes(x = .data$end, y = 40, xend = start, yend = 40), colour = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
          geom_segment(data=grid_data, aes(x = .data$end, y = 20, xend = start, yend = 20), colour = "grey", alpha=1, size=0.3 , inherit.aes = FALSE ) +
          
          # Add text showing the value of each .8/.6/.4/.2 lines
          annotate("text", x = rep(max(data$id),4), y = c(20, 40, 60, 80), label = c("0.2", "0.4", "0.6", "0.8") , color="grey", size=3 , angle=0, fontface="bold", hjust=1) +
          
          geom_bar(aes(x=as.factor(.data$id), y=.data$value, fill=.data$group), stat="identity", alpha=0.5) +
          ylim(-50,max(na.omit(data$value))+10) +
          theme_minimal() +
          theme(
            legend.position = "none",
            axis.text = element_blank(),
            axis.title = element_blank(),
            panel.grid = element_blank(),
            plot.margin = unit(rep(1,4), "cm")
          ) +
          coord_polar() +
          geom_text(data=label_data, aes(x=.data$id, y=.data$value+3, label=.data$individual, hjust=.data$hjust), color="black", fontface="bold",alpha=0.6, size=2.5, angle= label_data$angle, inherit.aes = FALSE ) +
          #
          # Add base line information
          geom_segment(data=base_data, aes(x = .data$start, y = -5, xend = .data$end, yend = -5), colour = "black", alpha=0.8, size=0.6 , inherit.aes = FALSE )  +
          geom_text(data=base_data, aes(x = .data$title, y = -10, label=.data$group), colour = "black", alpha=0.8, size=3, fontface="bold", inherit.aes = FALSE)
        
        p
      }else{
        plot(1:10,1:10,xaxt="n",yaxt="n",bty="n",type="n",xlab="",ylab="",
             main = "After filtering, no connected node is left!")
      }
}