UpSet: Make the UpSet plot
In ComplexHeatmap: Make Complex Heatmaps

Description Usage Arguments Details Examples

Make the UpSet plot

UpSet(m,
    comb_col = "black",
    pt_size = unit(3, "mm"), lwd = 2,
    bg_col = "#F0F0F0", bg_pt_col = "#CCCCCC",
    set_order = order(set_size(m), decreasing = TRUE),
    comb_order = if(attr(m, "param")$set_on_rows) {
    order.comb_mat(m[set_order, ], decreasing = TRUE)
    } else {
    order.comb_mat(m[, set_order], decreasing = TRUE)
    },
    top_annotation = upset_top_annotation(m),
    right_annotation = upset_right_annotation(m),
    row_names_side = "left",
    ...)

`m`	A combination matrix returned by `make_comb_mat`. The matrix can be transposed to switch the position of sets and combination sets.
`comb_col`	The color for the dots representing combination sets.
`pt_size`	The point size for the dots representing combination sets.
`lwd`	The line width for the combination sets.
`bg_col`	Color for the background rectangles.
`bg_pt_col`	Color for the dots representing the set is not selected.
`set_order`	The order of sets.
`comb_order`	The order of combination sets.
`top_annotation`	A `HeatmapAnnotation` object on top of the combination matrix.
`right_annotation`	A `HeatmapAnnotation` object on the right of the combination matrix.
`row_names_side`	The side of row names.
`...`	Other arguments passed to `Heatmap`.

By default, the sets are on rows and combination sets are on columns. The positions of the two types of sets can be switched by transposing the matrix.

When sets are on rows, the default top annotation is the barplot showing the size of each combination sets and the default right annotation is the barplot showing the size of the sets. The annotations are simply constructed by HeatmapAnnotation and anno_barplot with some parameters pre-set. Users can check the source code of upset_top_annotation and upset_right_annotation to find out how the annotations are defined.

To change or to add annotations, users just need to define a new HeatmapAnnotation object. E.g. if we want to change the side of the axis and name on top annotation:

    Upset(..., top_annotation = 
        HeatmapAnnotation(
           "Intersection size" = anno_barplot(
               comb_size(m), 
               border = FALSE, 
               gp = gpar(fill = "black"), 
               height = unit(2, "cm"),
               axis_param = list(side = "right")
           ), 
           annotation_name_side = "right", 
           annotation_name_rot = 0)
    )

To add more annotations on top, users just add it in HeatmapAnnotation:

    Upset(..., top_annotation = 
        HeatmapAnnotation(
           "Intersection size" = anno_barplot(
               comb_size(m), 
               border = FALSE, 
               gp = gpar(fill = "black"), 
               height = unit(2, "cm"),
               axis_param = list(side = "right")
           ), 
           "anno1" = anno_points(...),
           "anno2" = some_vector, 
           annotation_name_side = "right", 
           annotation_name_rot = 0)
    )

And so is for the right annotations.

UpSet returns a Heatmap-class object, which means, you can add it with other heatmaps and annotations by + or %v%.

set.seed(123)
lt = list(a = sample(letters, 10),
          b = sample(letters, 15),
          c = sample(letters, 20))
m = make_comb_mat(lt)
UpSet(m)
UpSet(t(m))

m = make_comb_mat(lt, mode = "union")
UpSet(m)
UpSet(m, comb_col = c(rep(2, 3), rep(3, 3), 1))

# compare two UpSet plots
set.seed(123)
lt1 = list(a = sample(letters, 10),
          b = sample(letters, 15),
          c = sample(letters, 20))
m1 = make_comb_mat(lt1)
set.seed(456)
lt2 = list(a = sample(letters, 10),
          b = sample(letters, 15),
          c = sample(letters, 20))
m2 = make_comb_mat(lt2)

max1 = max(c(set_size(m1), set_size(m2)))
max2 = max(c(comb_size(m1), comb_size(m2)))

UpSet(m1, top_annotation = upset_top_annotation(m1, ylim = c(0, max2)),
    right_annotation = upset_right_annotation(m1, ylim = c(0, max1)),
    column_title = "UpSet1") +
UpSet(m2, top_annotation = upset_top_annotation(m2, ylim = c(0, max2)),
    right_annotation = upset_right_annotation(m2, ylim = c(0, max1)),
    column_title = "UpSet2")

Loading required package: grid
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ComplexHeatmap version 2.6.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
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