R/plots_density.R

In samWieczorek/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

#' Densityplot of quantitative proteomics data over samples.
#' 
#' @title Builds a densityplot from a dataframe
#' 
#' @param obj xxx
#' 
#' @param legend A vector of the conditions (one condition 
#' per sample).
#' 
#' @param pal xxx
#' 
#' @return A density plot
#' 
#' @author Samuel Wieczorek
#' 
#' @examples 
#' utils::data(Exp1_R25_pept, package='DAPARdata')
#' densityPlotD_HC(Exp1_R25_pept)
#' conds <- Biobase::pData(Exp1_R25_pept)$Condition
#' pal <- ExtendPalette(2, 'Dark2')
#' densityPlotD_HC(Exp1_R25_pept, pal=pal)
#' 
#' @import highcharter
#' 
#' @export
#' 
densityPlotD_HC <- function(obj, 
                            legend=NULL, 
                            pal = NULL){
  
  if (is.null(obj)) {
    warning('The dataset is NULL and cannot be shown')
    return(NULL)
  } else if (nrow(obj) == 0) {
    warning('The dataset is empty and cannot be shown')
    return(NULL)
  }
  
  qData <- Biobase::exprs(obj)
  conds <- Biobase::pData(obj)$Condition
  
  if (is.null(legend) ) { legend<- Biobase::pData(obj)[,"Condition"]}

  myColors <- NULL
  if (is.null(pal)){
    myColors <- GetColorsForConditions(conds, ExtendPalette(length(unique(conds))))
  } else {
    if (length(pal) != length(unique(conds))){
      warning("The color palette has not the same dimension as the number of samples. Set to default.")
      myColors <- GetColorsForConditions(conds, ExtendPalette(length(unique(conds))))
    } else 
      myColors <- GetColorsForConditions(conds, pal)
  }
  
  h1 <-  highchart() %>% 
    hc_title(text = "Density plot") %>% 
    my_hc_chart(chartType = "spline", zoomType="x") %>%
    hc_colors(myColors) %>%
    hc_legend(enabled = TRUE) %>%
    hc_xAxis(title = list(text = "log(Intensity)")) %>%
    hc_yAxis(title = list(text = "Density")) %>%
    hc_tooltip(headerFormat= '',
               pointFormat = "<b> {series.name} </b>: {point.y} ",
               valueDecimals = 2) %>%
    my_hc_ExportMenu(filename = "densityplot") %>%
    hc_plotOptions(
      series=list(
        animation=list(
          duration = 100
        ),
        connectNulls= TRUE,
        marker=list(
          enabled = FALSE)
      )
    )
 
  if (is.null(legend)) {
    legend <- paste0("series", 1:ncol(qData))
  }
  
  for (i in 1:ncol(qData)){
    tmp <- data.frame(x = density(qData[,i], na.rm = TRUE)$x, 
                      y = density(qData[,i], na.rm = TRUE)$y)
    
    h1 <- h1 %>% hc_add_series(data=list_parse(tmp), name=legend[i]) 
  }

  return(h1)
}