RVenn: A package for set operations for many sets.

Description

Set operations for many sets. The base functions for set operations in R can be used for only two sets. This package uses 'purr' to find the union, intersection and difference of three or more sets. This package also provides functions for pairwise set operations among several sets. Further, based on 'ggplot2' and 'ggforce', a Venn diagram can be drawn for two or three sets. For bigger data sets, a clustered heatmap showing presence/absence of the elements of the sets can be drawn based on the 'pheatmap' package. Finally, enrichment test can be applied to two sets whether an overlap is statistically significant or not.

Build a Venn object.

Description

Venn builds a Venn object from a list.

Usage

## S4 method for signature 'ANY'
Venn(sets)

Arguments

Value

A Venn object.

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
print(venn)

An S4 class to represent multiple sets.

Description

An S4 class to represent multiple sets.

Slots

sets

A list object containing vectors in the same type.

names

The names of the sets if it has names. If the list doesn't have names, the sets will be named as "Set_1", "Set_2", "Set_3" and so on.

Set difference.

Description

discern returns the difference between two group of sets selected from a Venn object. If multiple sets are chosen for the slices, union of those sets will be used.

Usage

## S4 method for signature 'Venn'
discern(venn, slice1, slice2 = "all")

Arguments

Value

A vector showing the difference between slice1 and slice2.

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
discern(venn, slice1 = 1)
discern(venn, slice1 = c(1, 2), slice2 = 3)

Pairwise difference of many sets.

Description

discern_pairs returns the pairwise differences of the sets in a Venn object.

Usage

## S4 method for signature 'Venn'
discern_pairs(venn, slice = "all")

Arguments

Value

A list showing the pairwise differences of the sets.

Examples

venn = Venn(list(letters[1:10], letters[3:12],
                 letters[6:15], letters[9:18]))
discern_pairs(venn)
discern_pairs(venn, slice = 1:3)

Perform an enrichment test.

Description

Calculate the p-value of occurrence of an overlap between two sets by chance.

Usage

## S4 method for signature 'Venn'
enrichment_test(venn, set1, set2, univ = "all",
  n = 10000, seed = 42)

Arguments

Details

This type of analysis can also be performed by hypergeometric test or Fisher's exact test. Here, the approach is similar to that described in (Austin et al., 2016). Briefly, the test is based on randomly generation of sets with equal size to set1 from the background (universal) set. After creating n (default is 10,000) random sets, the overlap between these and set2 is calculated to make a null distribution. When this distribution is true, the probability of seeing an overlap at least as extreme as what was observed (overlap between set1 and set2) will be returned as the p-value.

Value

Returns a list containing the probability (Significance) of occurrence of an overlap between two sets by chance and the number of occurrences (Overlap_Counts) in randomly generated sets.

Examples

set1 = c(1:20, letters[1:10])
set2 = letters[-26]
univ = unique(c(set1, set2, 21:200))
venn = Venn(list(set1, set2, univ))
e = enrichment_test(venn, 1, 2)
e$Significance

Draw the Venn diagram.

Description

Draw the Venn diagram for 2 or 3 sets.

Usage

## S4 method for signature 'Venn'
ggvenn(venn = "Venn", slice = "all",
  fill = c("gold", "dodgerblue3", "deeppink"), alpha = 0.5,
  thickness = 1.5)

Arguments

Details

This function is based on the packages 'ggplot2' and 'ggforce.' It has been designed for 2 or 3 sets because Venn diagrams are terrible for showing the interactions of 4 or more sets. If you need to visualize such interactions, consider using setmap.

Value

The function returns the plot in ggplot2 style.

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
ggvenn(venn)
ggvenn(venn, slice = c(1, 2), thickness = 0, alpha = 0.3)

Intersection of many sets.

Description

overlap returns the same elements of the sets in a Venn object.

Usage

## S4 method for signature 'Venn'
overlap(venn, slice = "all")

Arguments

Value

A vector showing the intersection of the sets.

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
overlap(venn)
overlap(venn, slice = c(1, 2))

Pairwise intersections of many sets.

Description

overlap_pairs returns the pairwise intersections of the sets in a Venn object.

Usage

## S4 method for signature 'Venn'
overlap_pairs(venn, slice = "all")

Arguments

Value

A list showing the pairwise intersections of the sets.

Examples

venn = Venn(list(letters[1:10], letters[3:12],
                 letters[6:15], letters[9:18]))
overlap_pairs(venn)
overlap_pairs(venn, slice = 1:3)

Draw a clustered heatmap showing presence/absence of the elements.

Description

This function is based on the package 'pheatmap'. ggvenn function is useful for 2-3 sets, if you need to show interactions between many sets, you can show the presence/absence of the elements among all the sets and cluster both the sets and the elements based on Jaccard distances.

Usage

## S4 method for signature 'Venn'
setmap(venn, slice = "all", element_clustering = TRUE,
  set_clustering = TRUE, method = "average", legend = TRUE,
  title = NA, element_fontsize = 10, set_fontsize = 10)

Arguments

Value

Presence/absence heatmap of the sets.

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15], letters[9:16],
letters[15:25], letters[12:20]))
setmap(venn)
setmap(venn, slice = 1:4, element_clustering = FALSE, set_clustering = FALSE)

Union of many sets.

Description

unite returns the union of the sets in a Venn object.

Usage

## S4 method for signature 'Venn'
unite(venn, slice = "all")

Arguments

Value

A vector showing the union of the sets.

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
unite(venn)
unite(venn, slice = c(1, 2))

Pairwise unions of many sets.

Description

unite_pairs returns the pairwise unions of the sets in a Venn object.

Usage

## S4 method for signature 'Venn'
unite_pairs(venn, slice = "all")

Arguments

Value

A list showing the pairwise unions of the sets.

Examples

venn = Venn(list(letters[1:10], letters[3:12],
                 letters[6:15], letters[9:18]))
unite_pairs(venn)
unite_pairs(venn, slice = 1:3)