ComplexHeatmap's UpSet plots: how to convert a binary matrix into a list of sets
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moldach ▴ 20
@moldach-8829
Last seen 16 months ago
Canada/Montreal/Douglas Mental Health I…

In chapter 8 of the ComplexHeatmap manual, for UpSet plots, it describes a method of converting a list of sets where each set is a vector into a binary matrix where rows are elements and columns are sets using the list_to_matrix() function.

lt = list(set1 = c("a", "b", "c"),
          set2 = c("b", "c", "d", "e"))
mat = list_to_matrix(lt)
mat

Which looks like this

##   set1 set2
## a    1    0
## b    1    1
## c    1    1
## d    0    1
## e    0    1

How can one go in the other direction, convert the matrix back to a list of sets where each is unique, e.g.:

lt = list(set1 = c("a", "b", "c"),
          set2 = c("b", "c", "d", "e"))

I've got a binary matrix from consensus variants calls that was created using SURVIVOR and have already created a figure using ComplexHeatmap and would like to make a comparable figure using UpSet.js and it only accepts such input, e.g.:

devtools::install_url("https://github.com/upsetjs/upsetjs_r/releases/latest/download/upsetjs.tar.gz")
library(upsetjs)
listInput <- list(one = c(1, 2, 3, 5, 7, 8, 11, 12, 13), two = c(1, 2, 4, 5, 10), three = c(1, 5, 6, 7, 8, 9, 10, 12, 13))
upsetjs() %>% fromList(listInput) %>% interactiveChart()
ComplexHeatmap UpSet • 249 views
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like apply(mat, 2, function(x) rownames(mat)[x > 0])?

or apply(mat, 2, function(x) which(x > 0))?

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