Issue with fill colours for set sizes

[spencsa]

**I would like to change the fill colours for the set size bars, to produce a stacked bar chart. I have developed my code based on the example coding here (https://krassowski.github.io/complex-upset/articles/Examples_R.html#change-position-and-add-fill).

However, I am unable to change the colours (either by stipulating exact colours or by using scale fill brewer palettes) - when I try other colours, the bars always come out as grey**

Code

upset <- upset(
  mm1, disease_names, width_ratio=0.2, height_ratio = 0.7,
  base_annotations=list(
    #Intersection size and annotations)
    'Intersection size'=intersection_size(mode = 'exclusive_intersection',
                                          text_mapping=aes(
                                            label=paste0(!!size, '\n(', round(!!get_size_mode('exclusive_intersection')/nrow * 100), '%', ')'
                                            )
                                          ), text=list( 
                                            size = 2.5), size=0.8, 
                                          mapping=aes(fill='bars_color')
    ) + ylab("Prevalence") 
    + scale_y_continuous(labels=function(x) paste0(x/nrow*100, "%"), breaks = seq(0,0.30*nrow,0.10*nrow), limits = c(0,0.30*nrow))
    + scale_fill_manual(values=c('bars_color'= NA), guide='none')
    + theme(plot.background = element_rect(color = 'white', fill = 'white'), 
            element_line(linewidth = 0, colour = 'white'))
  ), 
  #sets and set annotations
  encode_sets=FALSE,  # for annotate() to select the set by name disable encoding
  set_sizes=(
    upset_set_size(position='right', 
                   # add colours to the set sizes. THIS IS THE SECTION THAT DOESN'T SEEM TO BE WORKING 
                   geom=geom_bar(
                     aes(fill=mm_count2) + scale_colour_manual(values = c(
                       "0"= 'steelblue1',
                       "1"= 'firebrick1',
                       "2" = 'violetred3',
                       "3" = 'royalblue2',
                       "4" = 'firebrick', 
                       "5"= 'darkmagenta'))))
    + geom_text(aes(label=paste0(..count.., ' (', round(..count../nrow*100), '%', ')')), 
                stat='count', hjust =1.1, vjust = "middle",  size = 2.5, nudge_y = 80) 
    + scale_y_continuous(labels=function(x) paste0(x/nrow*100, "%"), breaks = seq(0,0.50*nrow,0.20*nrow), limits = c(0,0.50*nrow))
    # you can also add annotations on top of bars:
    + expand_limits(y=400)
    + theme(axis.text.x=element_text(angle=45))
    + ylab('Prevalence of individual diseases')
  ), 
  sort_sets = 'FALSE',
  sort_intersections_by=c('degree', 'cardinality'),
  ggtitle('Full data set'),
  sort_intersections = 'ascending',
  guides='over',
  # colour arrangements for intersection matrix (this is based on one of your previous threads)
  queries= c(
    query_by_degree(
      mm1, disease_names,
      mode=mode,
      matrix=intersection_matrix(
        geom=geom_point(shape='circle filled', size=10)),
      params_by_degree=list(
        '0'=list(color = 'steelblue1', fill='steelblue1'),
        '1'=list(color = 'firebrick1', fill='firebrick1'),
        '2'=list(color = 'violetred3', fill='violetred3'),
        '3'=list( color = 'royalblue2',fill='royalblue2'),
        '4'=list(color = 'firebrick',fill='firebrick'), 
        '5'=list(color = 'darkmagenta', fill='darkmagenta')), shared=list(
          only_components=c("intersections_matrix", "Intersection size", "Set size"),
          color='turquoise'))
  )
)

---

---

ComplexUpset version: x.x.x

R version details

```R ```

R session information

```R ```

[krassowski]

scale_colour_manual() appears to be in an incorrect position, it should not be added to aes() but after upset_set_size() as is scale_y_continuous() in your example.

[spencsa]

Thank you for the quick response. Really appreciate that.

Unfortunately the set sizes plot seems to have reverted to the default colours (the same as in your example here: https://krassowski.github.io/complex-upset/articles/Examples_R.html#change-position-and-add-fill.)

Code below. Any ideas?

upset(
  mm1, disease_names, width_ratio=0.2, height_ratio = 0.7,
  base_annotations=list(
    #Intersection size and annotations)
    'Intersection size'=intersection_size(mode = 'exclusive_intersection',
                                          text_mapping=aes(
                                            label=paste0(!!size, '\n(', round(!!get_size_mode('exclusive_intersection')/nrow * 100), '%', ')'
                                            )
                                          ), text=list( 
                                            size = 2.5), size=0.8, 
                                          mapping=aes(fill='bars_color')
    ) + ylab("Prevalence") 
    + scale_y_continuous(labels=function(x) paste0(x/nrow*100, "%"), breaks = seq(0,0.30*nrow,0.10*nrow), limits = c(0,0.30*nrow))
    + scale_fill_manual(values=c('bars_color'= NA), guide='none')
    + theme(plot.background = element_rect(color = 'white', fill = 'white'), 
            element_line(linewidth = 0, colour = 'white'))
  ), 
  #sets and set annotations
  encode_sets=FALSE,  # for annotate() to select the set by name disable encoding
  set_sizes=(
    upset_set_size(position='right', 
                   # add colours to the set sizes
                   geom=geom_bar(
                     aes(fill=mm_count2, x = group)))
    + scale_colour_manual(values = c(
      "0"= 'steelblue1',
      "1"= 'firebrick1',
      "2" = 'violetred3',
      "3" = 'royalblue2',
      "4" = 'firebrick', 
      "5"= 'darkmagenta')) 
    + geom_text(aes(label=paste0(..count.., ' (', round(..count../nrow*100), '%', ')')), 
                stat='count', hjust =1.1, vjust = "middle",  size = 2.5, nudge_y = 80) 
    + scale_y_continuous(labels=function(x) paste0(x/nrow*100, "%"), breaks = seq(0,0.50*nrow,0.20*nrow), limits = c(0,0.50*nrow))
    # you can also add annotations on top of bars:
    + expand_limits(y=400)
    + theme(axis.text.x=element_text(angle=45))
    + ylab('Prevalence of individual diseases')
  ), 
  sort_sets = 'FALSE',
  sort_intersections_by=c('degree', 'cardinality'),
  ggtitle('Full data set'),
  sort_intersections = 'ascending',
  guides='over',
  # colour arrangements for intersection matrix
  queries= c(
    query_by_degree(
      mm1, disease_names,
      mode=mode,
      matrix=intersection_matrix(
        geom=geom_point(shape='circle filled', size=10)),
      params_by_degree=list(
        '0'=list(color = 'steelblue1', fill='steelblue1'),
        '1'=list(color = 'firebrick1', fill='firebrick1'),
        '2'=list(color = 'violetred3', fill='violetred3'),
        '3'=list( color = 'royalblue2',fill='royalblue2'),
        '4'=list(color = 'firebrick',fill='firebrick'), 
        '5'=list(color = 'darkmagenta', fill='darkmagenta')), shared=list(
          only_components=c("intersections_matrix", "Intersection size", "Set size"),
          color='turquoise'))
  )
)

[spencsa]

worked it out. error in scale_fill_manual, where previously it was scale_colour_manual.

Thanks for your help!