Skip to contents

UpSet chart filter helper functions

Source: R/annotation_upset_chart_class.R
upset_filters.Rd

These functions create filters for the annotation_upset_chart class to control which intersections are displayed in UpSet plots. Each function returns a filter function that can be used with the filter parameter.

Usage

upset_min_size(min_size)

upset_min_groups(min_groups)

upset_max_groups(max_groups)

upset_intersections(combinations)

Arguments

min_size

numeric The minimum number of items in an intersection

min_groups

numeric The minimum number of groups in an intersection

max_groups

numeric The maximum number of groups in an intersection

combinations

character Vector of specific intersection combinations to include (e.g., c("A/B", "B/C"))

Value

A function that takes region_data as input and returns a logical vector indicating which intersections to keep.

Details

These filter functions work by analyzing the region data from the Venn diagram to determine which intersections meet the specified criteria:

  • upset_min_size(): Filters intersections based on the number of items

  • upset_min_groups(): Filters intersections based on the minimum number of groups involved

  • upset_max_groups(): Filters intersections based on the maximum number of groups involved

  • upset_intersections(): Filters to show only specific intersection combinations (e.g., "A/B", "B/C", "A/B/C")

For complex filtering logic, create custom filter functions:


# Single filter
filter = upset_min_size(5)

# Specific combinations only
filter = upset_intersections(c("A/B", "B/C"))

# Custom filter function with AND logic
custom_filter <- function(region_data) {
  region_data$count >= 3 & region_data$count <= 10 & grepl("A", region_data$name)
}

# Custom filter function with OR logic
or_filter <- function(region_data) {
  region_data$count >= 5 | grepl("B/C", region_data$name)
}

Examples

# create a filter function that keeps intersections with 5+ items
f <- upset_min_size(5)
is.function(f)
#> [1] TRUE

# \donttest{
# Filter to show only intersections with 5+ items
C <- annotation_upset_chart(factor_name = "V1", filter = upset_min_size(5))

# Filter to show only intersections involving 3+ groups
C <- annotation_upset_chart(factor_name = "V1", filter = upset_min_groups(3))

# Filter to show only intersections involving 2-4 groups (custom function)
group_range_filter <- function(region_data) {
  group_counts <- sapply(region_data$name, function(x) {
    if (x == "") return(0)
    groups <- strsplit(x, "/")[[1]]
    length(groups)
  })
  group_counts >= 2 & group_counts <= 4
}
C <- annotation_upset_chart(factor_name = "V1", filter = group_range_filter)

# Filter to show only specific combinations
C <- annotation_upset_chart(factor_name = "V1", 
                          filter = upset_intersections(c("A/B", "B/C")))

# Custom filter combining size and group criteria
size_and_group_filter <- function(region_data) {
  region_data$count >= 3 & sapply(region_data$name, function(x) {
    if (x == "") return(FALSE)
    groups <- strsplit(x, "/")[[1]]
    length(groups) >= 2
  })
}
C <- annotation_upset_chart(factor_name = "V1", filter = size_and_group_filter)
# }