setting size of mainbar.y.max

[pagyeman]

Hi, thanks so much for the great package!

it seems that mainbar.y.max can not accept values that are less than the size of the largest intersection size bar. If doing so I get the following error: "Error: Aesthetics must be either length 1 or the same as the data (59): fill In addition: Warning message: Removed 4 rows containing missing values (position_stack)."

I was wondering whether you implemented this with coord_cartesian() in ggplot2 or not. If yes I was wondering why I might get this error.

BW
Philipp

[JakeConway]

Hello Philipp, the intersection size bar plot is not implemented with coord_cartesian(). The ggplot function for the main bar graph can be found in at the bottom of the MainBar.R file (https://github.com/hms-dbmi/UpSetR/blob/master/R/MainBar.R)

[pagyeman]

Hello Jake,
Not sure whether this is helpful, but below is a slight adaption of your Make_main_bar function that uses coord_cartesian() to change y-axis dimensions of the bar plot (code can probably be optimized, but it worked for me). This will not throw an error, even if the value for mainbar.y.max is smaller than the largest set. This was useful in my special use case.

Sorry for sending the code snippet as is, but wasn't sure how this is properly done.

##
  # if ymax is set by the user, save in a different variable adding the 10% space
  if(is.null(ymax) == F){
    y_coord <- ymax + 0.1 * ymax
  }
  # ten_perc creates appropriate space above highest bar so number doesnt get cut off
  ten_perc <- ((max(Main_bar_data$freq)) * 0.1)
 # currently ymax needs to be calculated in any case, because scale_y_continuous() is used, change?
  ymax <- max(Main_bar_data$freq) + ten_perc
  # if ymax is not set by the user then y_coord should equal calculated ymax
  if(is.null(ymax) == T){
  y_coord <- ymax
  }
  Main_bar_plot <- (ggplot(data = Main_bar_data, aes_string(x = "x", y = "freq")) 
                    + geom_bar(stat = "identity", width = 0.6, 
                               fill = Main_bar_data$color)
                    + scale_x_continuous(limits = c(0,(nrow(Main_bar_data)+1 )), expand = c(0,0),
                                         breaks = NULL)
                    + scale_y_continuous(limits = c(0, ymax), 
                                         expand = c(c(0,0), c(0,0)))
                    + xlab(NULL) + ylab(ylabel) +labs(title = NULL)
                    + theme(panel.background = element_rect(fill = "white"),
                            plot.margin = unit(c(0.5,0.5,0.19,0.5), "lines"), panel.border = element_blank(),
                            axis.title.y = element_text(vjust = -0.8, size = 8.3), axis.text.y = element_text(vjust=0.3,
                                                                                                            size=7 ))
                    + coord_cartesian(ylim = c(0, y_coord)))  # use coord_cartesian to zoom in on plot
  if((show_num == "yes") || (show_num == "Yes")){
    Main_bar_plot <- (Main_bar_plot + geom_text(aes_string(label = "freq"), size = 2.2, vjust = -1,
                                                angle = number_angles, colour = Main_bar_data$color))
  }