Perform enrichtment analysis from a weave

Usage

weave_coverage(
  x,
  .path,
  .data = NULL,
  metric = c("set_count", "set_size", "coverage", "complete"),
  out.format = c("LinkMap", "matrix"),
  .data_column = "row.names"
)

test_enrichment(x, log_base = 2L)

Arguments

x: A LinkMap with coverage metadata from weave_coverage().
.path: Either a formula or a character vector of length 2 with the names of the desired combination of feature types.
.data: Optional Character vector. Lists observed features from the found within the first element of .path. Alternatively, a data.frame with the same information. (Also see .data_column argument).
metric: Character scalar. One or more of 'set_count', 'set_size', 'coverage', 'complete'.
out.format: Character scalar. One of 'LinkMap', 'matrix'.
.data_column: Character scalar. if .data is a table, where to find feature IDs
log_base: Integer. Base of logarithm for log-fold (default: 2).

Value

a LinkMap or matrix with the desired coverage information in the @metadata slot.

Examples

set.seed(2612)
# Draw five cards from a deck
drawn  <- draw_cards(5)
drawn
#> [1] "Jack♦️" "5♥️"    "King♠️" "7♥️"    "6♦️"   
scores <- poker_scores()
scores
#> A MultiFactor::MultiFactor list S7_object,
#>     4 feature types across 3 LinkMaps.
#> 
#>               card rank suit straight
#> card2rank       52   13    .        .
#> card2suit       52    .    4        .
#> rank2straight    .   13    .       10
#> 
#> Values represent unique feature names in that LinkMap.
#> 
#> @ levels:
#>  $ card     : 52 Levels: Ace♥️ ... King♣️ 
#>  $ rank     : 13 Levels: Ace ... King 
#>  $ suit     :  4 Levels: hearts spades diamonds clubs 
#>  $ straight : 10 Levels: Ace to 5 ... Royal straight 

# Now enrich input
result <- weave_coverage(
x = scores, .path = card ~ suit, .data = drawn, metric = "set_count"
)

result
#> A MultiFactor::LinkMap data.frame S7_object: 52 rows.
#>    card  suit
#> 1  Ace♣️ clubs
#> 2    2♣️ clubs
#> 3    3♣️ clubs
#> 4    4♣️ clubs
#> 5    5♣️ clubs
#> 6    6♣️ clubs
#> 7    7♣️ clubs
#> 8    8♣️ clubs
#> 9    9♣️ clubs
#> 10  10♣️ clubs
#>  + 42 more rows. Use `print(n = ...)` to see more rows.
#> 
#> @ levels:   2 variables: 
#>  $ card : 52 Levels: Ace♥️ ... King♣️ 
#>  $ suit :  4 Levels: hearts spades diamonds clubs 
#> 
#> @ metadata: 2 variables: 
#> List of 2
#>  $ observed : logi  FALSE FALSE FALSE FALSE FALSE FALSE ...
#>  $ set_count: int  0 0 0 0 0 0 0 0 0 0 ...

# Now let's spike our hand with a royal straight flush
cheat <- draw_cards()[c(10, 11, 12, 13, 1)]
cheat
#> [1] "10♥️"    "Jack♥️"  "Queen♥️" "King♥️"  "Ace♥️"  

.path = card ~ straight
result <- weave_coverage(scores, card ~ straight, .data = cheat)
result
#> A MultiFactor::LinkMap data.frame S7_object: 200 rows.
#>    card straight
#> 1  Ace♥️ Ace to 5
#> 2    2♥️ Ace to 5
#> 3    3♥️ Ace to 5
#> 4    4♥️ Ace to 5
#> 5    5♥️ Ace to 5
#> 6  Ace♠️ Ace to 5
#> 7    2♠️ Ace to 5
#> 8    3♠️ Ace to 5
#> 9    4♠️ Ace to 5
#> 10   5♠️ Ace to 5
#>  + 190 more rows. Use `print(n = ...)` to see more rows.
#> 
#> @ levels:   2 variables: 
#>  $ card     : 52 Levels: Ace♥️ ... King♣️ 
#>  $ straight : 10 Levels: Ace to 5 ... Royal straight 
#> 
#> @ metadata: 5 variables: 
#> List of 5
#>  $ observed : logi  TRUE FALSE FALSE FALSE FALSE FALSE ...
#>  $ set_count: int  1 1 1 1 1 1 1 1 1 1 ...
#>  $ set_size : int  20 20 20 20 20 20 20 20 20 20 ...
#>  $ coverage : num  0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 ...
#>  $ complete : logi  FALSE FALSE FALSE FALSE FALSE FALSE ...
test_enrichment(result)
#>                  expected observed fold    log_fold     p.value      p.adj
#> Ace to 5       0.09615385     0.05 0.52 -0.94341647 0.922516699 1.00000000
#> 2 to 6         0.09615385     0.00 0.00        -Inf 1.000000000 1.00000000
#> 3 to 7         0.09615385     0.00 0.00        -Inf 1.000000000 1.00000000
#> 4 to 8         0.09615385     0.00 0.00        -Inf 1.000000000 1.00000000
#> 5 to 9         0.09615385     0.00 0.00        -Inf 1.000000000 1.00000000
#> 6 to 10        0.09615385     0.05 0.52 -0.94341647 0.922516699 1.00000000
#> 7 to Jack      0.09615385     0.10 1.04  0.05658353 0.645790624 1.00000000
#> 8 to Queen     0.09615385     0.15 1.56  0.64154603 0.283184043 0.94394681
#> 9 to King      0.09615385     0.20 2.08  1.05658353 0.065620094 0.32810047
#> Royal straight 0.09615385     0.25 2.60  1.37851162 0.005965463 0.05965463