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feat: add extractCombinationsImpl
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an improved distinct intersection from data frame
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@sgratzl
sgratzl committed Feb 11, 2021
1 parent debff1b commit 5242a90
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Showing 2 changed files with 120 additions and 35 deletions.
124 changes: 92 additions & 32 deletions r_package/R/data.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,8 @@ generateCombinationsImpl = function(sets,
order.by,
limit,
colors = NULL,
symbol = "&") {
symbol = "&",
store.elems = TRUE) {
combinations = list()
set_f = if (c_type == "union")
union
Expand All @@ -79,11 +80,9 @@ generateCombinationsImpl = function(sets,
lsets = length(sets)
all_indices = 1:lsets
cc = colorLookup(colors)
max_sets = ifelse(is.null(max), lsets, max)

for (l in min:(if (is.null(max))
lsets
else
max)) {
for (l in min:max_sets) {
combos = combn(all_indices, l, simplify = FALSE)
for (combo in combos) {
indices = unlist(combo)
Expand Down Expand Up @@ -113,7 +112,7 @@ generateCombinationsImpl = function(sets,
name = c_name,
color = cc(c_name),
type = c_type,
elems = elems,
elems = ifelse(store.elems, elems, c()),
cardinality = length(elems),
setNames = set_names
),
Expand Down Expand Up @@ -195,7 +194,9 @@ fromList = function(upsetjs,
else
sorted_sets

gen = if (!is.null(c_type) && c_type == "none") list() else if (isVennDiagram(upsetjs) || isKarnaughMap(upsetjs)) {
gen = if (!is.null(c_type) && c_type == "none") {
list()
} else if (isVennDiagram(upsetjs) || isKarnaughMap(upsetjs)) {
generateCombinationsImpl(
gen_sets,
ifelse(is.null(c_type), 'distinctIntersection', c_type),
Expand Down Expand Up @@ -343,7 +344,6 @@ extractSetsFromDataFrame = function(df,
order.by = "cardinality",
limit = NULL,
colors = NULL,
c_type = NULL,
store.elems = TRUE) {
stopifnot(is.data.frame(df))
stopifnot((
Expand Down Expand Up @@ -376,11 +376,51 @@ extractSetsFromDataFrame = function(df,
c())
sets = lapply(set_names, toSet)

sorted_sets = sortSets(sets, order.by = order.by, limit = limit)
if (is.null(limit))
sets
else
sorted_sets
sortSets(sets, order.by = order.by, limit = limit)
}


extractCombinationsImpl = function(df,
sets,
empty,
order.by,
colors = NULL,
symbol = "&",
store.elems = TRUE) {
combination_names = c()
lookup = new.env(hash=TRUE, parent=emptyenv())
all_set_names = sapply(1:length(sets), function(i) sets[[i]]$name)
if (is.list(all_set_names)) {
all_set_names = unlist(all_set_names)
}
cc = colorLookup(colors)

elems = rownames(df)
df_sets = df[, all_set_names]
c_name = apply(df_sets, 1, function(r) paste(all_set_names[as.logical(r)], collapse=symbol))

dd = aggregate(elems, list(c_name = c_name), function(r) {
r
})
set_names = str_split(dd$c_name, fixed(symbol))
set_colors = cc(dd$c_name)

combinations = lapply(1:nrow(dd), function(i) {
elems = as.character(unlist(dd[i, 'x']))
structure(
list(
name = dd[i, 'c_name'],
color = set_colors[i],
type = 'distinctIntersection',
elems = elems,
cardinality = length(elems),
setNames = unlist(set_names[i])
),
class = "upsetjs_combination"
)
})
names(combinations) = NULL
sortSets(combinations, order.by, limit)
}

#'
Expand Down Expand Up @@ -408,7 +448,8 @@ fromDataFrame = function(upsetjs,
shared = NULL,
shared.mode = "click",
colors = NULL,
c_type = NULL) {
c_type = NULL,
store.elems = TRUE) {
checkUpSetCommonArgument(upsetjs)
stopifnot(is.data.frame(df))
stopifnot((
Expand All @@ -429,36 +470,55 @@ fromDataFrame = function(upsetjs,

cc = colorLookup(colors)

sorted_sets = extractSetsFromDataFrame(df, attributes, order.by, limit, colors)

gen_sets = if (is.null(limit))
sets
else
sorted_sets
sorted_sets = extractSetsFromDataFrame(df, attributes, order.by, limit, colors, store.elems = store.elems)

elems = rownames(df)

gen = if (!is.null(c_type) && c_type == "none") list() else if (isVennDiagram(upsetjs) || isKarnaughMap(upsetjs)) {
generateCombinationsImpl(
gen_sets,
ifelse(is.null(c_type), 'distinctIntersection', c_type),
0,
NULL,
TRUE,
'degree',
NULL,
colors
gen = if (!is.null(c_type) && c_type == "none") {
list()
} else if (isVennDiagram(upsetjs) || isKarnaughMap(upsetjs)) {
if (is.null(c_type) || c_type == 'distinctIntersection') {
extractCombinationsImpl(
df,
sorted_sets,
TRUE,
order.by,
colors,
store.elems = store.elems
)
} else {
generateCombinationsImpl(
sorted_sets,
ifelse(is.null(c_type), 'distinctIntersection', c_type),
0,
NULL,
TRUE,
'degree',
NULL,
colors,
store.elems = store.elems
)
}
} else if (!is.null(c_type) && c_type == 'distinctIntersection') {
extractCombinationsImpl(
df,
sorted_sets,
FALSE,
order.by,
colors,
store.elems = store.elems
)
} else {
generateCombinationsImpl(
gen_sets,
sorted_sets,
ifelse(is.null(c_type), 'intersection', c_type),
0,
NULL,
FALSE,
order.by,
NULL,
colors
colors,
store.elems = store.elems
)
}
props = list(
Expand Down
31 changes: 28 additions & 3 deletions r_package/tests/testthat/test-data.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -75,10 +75,35 @@ test_that("fromDataFrame", {
cc = u %>% getCombinations()
expect_equal(length(cc), 7)
expect_set(cc[[1]], 'one', 9)
expect_set(cc[[2]], 'two', 9)
expect_set(cc[[3]], 'three', 5)
expect_set(cc[[2]], 'three', 9)
expect_set(cc[[3]], 'two', 5)
expect_set(cc[[4]], 'one&three', 6)
expect_set(cc[[5]], 'one&two', 3)
expect_set(cc[[6]], 'three&two', 3)
expect_set(cc[[7]], 'one&three&two', 2)
expect_set(cc[[7]], 'one&three&two', 2)
})

test_that("fromDataFrame - distinctIntersection", {
dataFrame <- as.data.frame(list(
one=c(1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1),
two=c(1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0),
three=c(1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1)),
row.names=c('a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm'))

u = upsetjs_mock() %>% fromDataFrame(dataFrame, c_type = 'distinctIntersection', order.by='degree')
sets = u %>% getSets()
expect_equal(length(sets), 3)
expect_set(sets[[1]], 'one', 9)
expect_set(sets[[2]], 'three', 9)
expect_set(sets[[3]], 'two', 5)

cc = u %>% getCombinations()
expect_equal(length(cc), 7)
expect_set(cc[[1]], 'one', 2)
expect_set(cc[[2]], 'three', 2)
expect_set(cc[[3]], 'two', 1)
expect_set(cc[[4]], 'one&three', 4)
expect_set(cc[[5]], 'one&two', 1)
expect_set(cc[[6]], 'three&two', 1)
expect_set(cc[[7]], 'one&three&two', 2)
})

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