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feat: start AnchoredPinnedGInteractions and anchor methods
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| #' @importFrom InteractionSet GInteractions | ||
| #' @importFrom S4Vectors DataFrame | ||
| #' @importFrom S4Vectors Rle | ||
| #' @importFrom utils capture.output | ||
| #' @importFrom methods show | ||
| #' @include PinnedGInteractions-class.R | ||
| setClass("AnchoredPinnedGInteractions", | ||
| slot = c( | ||
| anchor = "character" | ||
| ), | ||
| contains = c("PinnedGInteractions") | ||
| ) | ||
|
|
||
| #' @importFrom InteractionSet GInteractions | ||
| #' @importFrom methods setMethod initialize | ||
| setMethod("initialize", "AnchoredPinnedGInteractions", function( | ||
| .Object, delegate = InteractionSet::GInteractions(), pin, anchor | ||
| ) { | ||
| stopifnot( | ||
| pin %in% c("anchors1", "first", "1", "anchors2", "second", "2") | ||
| ) | ||
| pin <- switch(pin, | ||
| "anchors1" = 1L, | ||
| "first" = 1L, | ||
| "1" = 1L, | ||
| "anchors2" = 2L, | ||
| "second" = 2L, | ||
| "2" = 2L | ||
| ) | ||
| .Object@delegate <- delegate | ||
| .Object@pin <- pin | ||
| .Object@anchor <- anchor | ||
| .Object | ||
| }) | ||
|
|
||
| setMethod("show", "AnchoredPinnedGInteractions", function(object) { | ||
| output <- c("", utils::capture.output(show(object@delegate))) | ||
| output[1] <- output[2] | ||
| output[2] <- paste0( | ||
| "Pinned on: `anchors", object@pin, | ||
| "` (anchored on: `", object@anchor, "`)" | ||
| ) | ||
| cat(output, sep = "\n") | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| #' @importFrom InteractionSet GInteractions | ||
| #' @importFrom S4Vectors DataFrame | ||
| #' @importFrom S4Vectors Rle | ||
| #' @importFrom utils capture.output | ||
| #' @importFrom methods show | ||
| #' @include DelegatingGInteractions-class.R | ||
| setClass("PinnedGInteractions", | ||
| slot = c( | ||
| pin = "integer" | ||
| ), | ||
| contains = c("DelegatingGInteractions") | ||
| ) | ||
|
|
||
| #' @importFrom InteractionSet GInteractions | ||
| #' @importFrom methods setMethod initialize | ||
| setMethod("initialize", "PinnedGInteractions", function( | ||
| .Object, delegate = InteractionSet::GInteractions(), pin | ||
| ) { | ||
| stopifnot( | ||
| pin %in% c("anchors1", "first", "1", "anchors2", "second", "2") | ||
| ) | ||
| pin <- switch(pin, | ||
| "anchors1" = 1L, | ||
| "first" = 1L, | ||
| "1" = 1L, | ||
| "anchors2" = 2L, | ||
| "second" = 2L, | ||
| "2" = 2L | ||
| ) | ||
| .Object@delegate <- delegate | ||
| .Object@pin <- pin | ||
| .Object | ||
| }) | ||
|
|
||
| setMethod("show", "PinnedGInteractions", function(object) { | ||
| output <- c("", utils::capture.output(show(object@delegate))) | ||
| output[1] <- output[2] | ||
| output[2] <- paste0("Pinned on: anchors", object@pin) | ||
| cat(output, sep = "\n") | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| #' Pin GInteractions by anchors set (anchors1 or anchors2). | ||
| #' | ||
| #' @param .data,x a (Grouped)GInteractions object | ||
| #' @param anchors Anchors to pin on ("first" or "second") | ||
| #' | ||
| #' @return a PinnedGInteractions object. | ||
| #' | ||
| #' @rdname ginteractions-pin | ||
| #' | ||
| #' @examples | ||
| #' gi <- read.table(text = " | ||
| #' chr1 11 20 chr1 21 30 | ||
| #' chr1 11 20 chr1 51 50 | ||
| #' chr1 11 30 chr1 51 50 | ||
| #' chr1 11 30 chr2 51 60", | ||
| #' col.names = c("seqnames1", "start1", "end1", "seqnames2", "start2", "end2")) |> | ||
| #' as_ginteractions() |> | ||
| #' mutate(type = c('cis', 'cis', 'cis', 'trans'), score = runif(4)) | ||
| #' | ||
| #' #################################################################### | ||
| #' # 1. Pin and modify anchors | ||
| #' #################################################################### | ||
| #' | ||
| #' gi |> pin("first") | ||
| #' | ||
| #' gi |> pin_by("first") | ||
| #' | ||
| #' gi |> pin_first() | ||
| #' | ||
| #' gi |> pin_anchors1() | ||
| #' | ||
| #' #################################################################### | ||
| #' # 2. Pin by second anchors | ||
| #' #################################################################### | ||
| #' | ||
| #' gi |> pin("second") | ||
| #' | ||
| #' gi |> pin_by("second") | ||
| #' | ||
| #' gi |> pin_second() | ||
| #' | ||
| #' gi |> pin_anchors2() | ||
| #' | ||
| #' #################################################################### | ||
| #' # 3. Unpin | ||
| #' #################################################################### | ||
| #' | ||
| #' gi |> pin("second") |> unpin() | ||
| #' | ||
| #' @export | ||
| setGeneric("pin", function(x, anchors) standardGeneric("pin")) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setMethod("pin", signature(x = "GInteractions", anchors = "character"), function(x, anchors) { | ||
| methods::new("PinnedGInteractions", x, anchors) | ||
| }) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setMethod("pin", signature(x = "GInteractions", anchors = "numeric"), function(x, anchors) { | ||
| if (!anchors %in% c(1, 2)) stop("`anchors` can only be set to `1` or `2`") | ||
| methods::new("PinnedGInteractions", x, as.character(anchors)) | ||
| }) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setMethod("pin", signature(x = "PinnedGInteractions", anchors = "missing"), function(x, anchors) { | ||
| x@pin | ||
| }) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setMethod("pin", signature(x = "PinnedGInteractions", anchors = "character"), function(x, anchors) { | ||
| methods::new("PinnedGInteractions", x@delegate, anchors) | ||
| }) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setMethod("pin", signature(x = "PinnedGInteractions", anchors = "numeric"), function(x, anchors) { | ||
| if (!anchors %in% c(1, 2)) stop("`anchors` can only be set to `1` or `2`") | ||
| methods::new("PinnedGInteractions", x@delegate, as.character(anchors)) | ||
| }) | ||
|
|
||
| #' @export | ||
| #' @rdname ginteractions-pin | ||
| setGeneric("pin_by", function(x, anchors) pin(x, anchors)) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| pin_first <- function(x) pin(x, 1) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| pin_second <- function(x) pin(x, 2) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| pin_anchors1 <- function(x) pin(x, 1) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| pin_anchors2 <- function(x) pin(x, 2) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setGeneric("unpin", function(x) standardGeneric("unpin")) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setMethod("unpin", signature(x = "PinnedGInteractions"), function(x) { | ||
| x@delegate | ||
| }) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setMethod("unpin", signature(x = "GInteractions"), function(x) { | ||
| x | ||
| }) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setGeneric("pinned_anchors", function(x) standardGeneric("pinned_anchors")) | ||
|
|
||
| #' @rdname ginteractions-pin | ||
| #' @export | ||
| setMethod("pinned_anchors", signature(x = "PinnedGInteractions"), function(x) { | ||
| id <- switch(pin(x), "1" = "first", "2" = "second") | ||
| InteractionSet::anchors(x@delegate, type = id) | ||
| }) |
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