plot.margin with size of saved plot

[erikagucciardo]

Hi!

Thanks for such a useful package!

I would like to be able to reduce the margins of the various plots but it seems that when I save the plot, the spaces between subplots don't get adjusted. It seems like the code I am using doesn't respond to plot.margin. I think it may be something to do with wrap and patchwork and/or the way I structured the themes, but I can't seem to figure it out. Any help will be greatly appreciated!

Below example of the same plot saved into two file sizes with ggsave.

Code:

plot = ComplexUpset::upset(
  data = Joint.all,
  intersect = Workflows,
  name = "",
  width_ratio = 0.1,
  wrap = FALSE,
  set_sizes = (upset_set_size(geom = geom_bar(fill = "black"))+
                 scale_y_continuous(limits = c(0,NA),
                                    expand = c(0.01,0),
                                    breaks = c(0,1000,2000,3000),
                                    labels = unit_format(unit = "K", scale = 1e-3, sep = ""))),
  base_annotations = list(
    'Intersection size (>1500)'= (
      intersection_size(text = list(size = 1, color = "black", vjust = -4.4))+
        scale_y_continuous(breaks = c(3000,3500),
                           labels = unit_format(unit = "K", scale = 1e-3, sep = ""),
                           expand = c(0.01,0))+
        coord_cartesian(ylim = c(3000, 3600),
                        expand = TRUE)+
        ylab('')),
    'Intersection size'=(
      intersection_size(text = list(size = 1., color = "black"))+
        scale_y_continuous(breaks = c(0, 10, 20, 30, 40, 50),
                           expand = c(0.01,0))+
        coord_cartesian(ylim = c(0, 50),
                        expand = TRUE))),
  annotations = list(
    "Patient" = (
      ggplot(mapping = aes(fill = Patient))+
        geom_bar(stat = "count", position = "fill")+
        scale_y_continuous(labels = scales::percent_format())+
        scale_fill_manual(values = c('1'='#006ba4',
                                     '2'='#ff800e',
                                     '3'='#ababab',
                                     '4'='#595959',
                                     '5'='#5f9ed1',
                                     '6'='#898989',
                                     '7'='#a2c8ec',
                                     '8'='#c85200',
                                     '9'='#ffbc79',
                                     '10'='#cfcfcf'))+
        ylab("Patient"))),
  matrix = (
    intersection_matrix(
      geom = geom_point(
        size = 0.2),
      segment = geom_segment(
        linewidth = 0.2))),
  themes = upset_modify_themes(
    list(
      'intersections_matrix' = theme(
        axis.text.x = element_blank(),
        axis.ticks.x = element_blank(),
        axis.title.y = element_blank(),
        axis.text.y = element_text(color = "black", size = 3, margin = margin(0,-2,0,0, "pt")),
        panel.grid = element_blank(),
        panel.background = element_blank(),
        plot.background = element_blank(),
        plot.margin = margin(0,0,0,0, "pt"),
        title = element_blank()),
      'Intersection size (>1500)' = theme(
        axis.text.x = element_blank(),
        axis.ticks.x = element_blank(),
        axis.title.x = element_blank(),
        panel.grid = element_blank(),
        axis.text.y = element_text(size = 4, color = "black", vjust = 0.5, margin = margin(0,1,0,0, "pt")),
        axis.line.y = element_line(colour = "black", linewidth = 0.2344, lineend="round"),
        axis.ticks.y = element_line(colour = "black", linewidth = 0.2344, lineend="round"),
        axis.ticks.length.y = unit(1, "pt"),
        legend.position = "none",
        panel.background = element_blank(),
        plot.background = element_blank(),
        plot.margin = margin(b = -50),
        title = element_blank()),
      'Intersection size' = list(
        theme_minimal(),
        theme(
          axis.text.x = element_blank(),
          axis.title.x = element_blank(),
          panel.grid = element_blank(),
          axis.title.y = element_text(size = 4, color = "black", margin = margin(0,-8,0,5, "pt")),
          axis.text.y = element_text(size = 4, color = "black", vjust = 0.5, margin = margin(0,1,0,0, "pt")),
          axis.line = element_line(colour = "black", linewidth = 0.2344, lineend="round"),
          axis.ticks.y = element_line(colour = "black", linewidth = 0.2344, lineend="round"),
          axis.ticks.length.y = unit(1, "pt"),
          legend.text = element_text(colour = "black",size = 4),
          legend.justification = "top",
          legend.position = "none",
          legend.title = element_blank(),
          legend.key.size = unit(6,"pt"),
          legend.spacing.x = unit(1,"pt"),
          legend.background = element_blank(),
          legend.box.margin = margin(0,0,0,0, "pt"),
          legend.margin = margin(0,0,0,0, "pt"),
          panel.background = element_blank(),
          panel.spacing.y = margin(0,0,0,0,"pt"),
          plot.background = element_blank(),
          plot.margin = margin(0,0,-50,0, "pt"),
          title = element_blank())),
      "Patient" = list(
        theme_minimal(),
        theme(
          axis.text.x = element_blank(),
          axis.title.x = element_blank(),
          axis.title.y = element_text(size = 4, color = "black", margin = margin(0,-8,0,5, "pt")),
          axis.text.y = element_text(size = 4, color = "black", vjust = 0.5, margin = margin(0,1,0,0, "pt")),
          axis.line = element_line(colour = "black", linewidth = 0.2344, lineend="round"),
          axis.ticks.y = element_line(colour = "black", linewidth = 0.2344, lineend="round"),
          axis.ticks.length.y = unit(1, "pt"),
          legend.text = element_text(colour = "black",size = 4),
          legend.justification = "top",
          legend.position = "none",
          legend.title = element_blank(),
          legend.key.size = unit(6,"pt"),
          legend.spacing.x = unit(1,"pt"),
          legend.background = element_blank(),
          legend.box.margin = margin(0,0,0,0, "pt"),
          legend.margin = margin(0,0,0,0, "pt"),
          panel.grid = element_blank(),
          panel.background = element_blank(),
          panel.spacing.y = margin(0,0,-50,0,"pt"),
          plot.background = element_blank(),
          plot.margin = margin(0,0,-20,0, "pt"),
          title = element_blank())),
      "overall_sizes" = list(
        theme_minimal(),
        theme(
          axis.title.y=element_blank(),
          axis.text.y=element_blank(),
          axis.ticks.y=element_blank(),
          axis.ticks.x = element_line(colour = "black", linewidth = 0.2344, lineend="round"),
          axis.ticks.length.x = unit(1, "pt"),
          axis.title.x = element_text(size = 4, color = "black", vjust = 0.5, margin = margin(-2,0,0,0, "pt")),
          axis.text.x = element_text(size = 4, color = "black", vjust = 0.5, margin = margin(-1,0,0,0, "pt")),
          panel.background = element_blank(),
          panel.grid = element_blank(),
          plot.margin = margin(r = 0))),
      default = list(
        theme_minimal(),
        theme(
          axis.text.x=element_blank(),
          axis.title.x=element_blank())
      ))),
  sort_intersections_by = "degree",
  guides = "keep") + 
  patchwork::plot_layout(
    heights = c(0.7, 0.3, 1, 0.7), nrow = 4)
plot
ggsave(plot = plot, file = "Figure_small.pdf", device = cairo_pdf, height = 2.7, width = 4, units = "in", dpi = 600, 
       path = panelspath)

ggsave(plot = plot, file = "Figure_big.pdf", device = cairo_pdf, height = 27, width = 40, units = "in", dpi = 600, 
       path = panelspath)

Figure_big.pdf
Figure_small.pdf