doc: fix lines > 80 characters

R/AllGenerics.R

@@ -1,6 +1,8 @@
 #' @rdname replace_anchors
 #' @export
-setGeneric("replace_anchors", function(x, id, value) standardGeneric("replace_anchors"))
+setGeneric("replace_anchors", 
+    function(x, id, value) standardGeneric("replace_anchors")
+)
 
 
 
@@ -27,7 +29,9 @@ setGeneric("unpin", function(x) standardGeneric("unpin"))
 setGeneric("annotate", function(x, y, by) standardGeneric("annotate"))
 #' @rdname ginteractions-annotate
 #' @export
-setGeneric("annotate_directed", function(x, y, by) standardGeneric("annotate_directed"))
+setGeneric("annotate_directed", 
+    function(x, y, by) standardGeneric("annotate_directed")
+)
 
 
 

R/anchor.R

@@ -88,19 +88,28 @@ anchor_5p.PinnedGInteractions <- function(x) {
 #' @name ginteractions-anchor
 #' @export
 anchor_start.AnchoredPinnedGInteractions <- function(x) {
-    new("AnchoredPinnedGInteractions", unanchor(x), pin = pin(x), anchor = "start")
+    new(
+        "AnchoredPinnedGInteractions", 
+        unanchor(x), pin = pin(x), anchor = "start"
+    )
 }
 
 #' @name ginteractions-anchor
 #' @export
 anchor_end.AnchoredPinnedGInteractions <- function(x) {
-    new("AnchoredPinnedGInteractions", unanchor(x), pin = pin(x), anchor = "end")
+    new(
+        "AnchoredPinnedGInteractions", 
+        unanchor(x), pin = pin(x), anchor = "end"
+    )
 }
 
 #' @name ginteractions-anchor
 #' @export
 anchor_center.AnchoredPinnedGInteractions <- function(x) {
-    new("AnchoredPinnedGInteractions", unanchor(x), pin = pin(x), anchor = "center")
+    new(
+        "AnchoredPinnedGInteractions", 
+        unanchor(x), pin = pin(x), anchor = "center"
+    )
 }
 
 #' @name ginteractions-anchor

R/annotate.R

@@ -20,7 +20,10 @@
 #' gi <- read.table(text = "  
 #'     chr1 11 20 - chr1 21 30 + 
 #'     chr1 21 30 + chr2 51 60 +",  
-#'     col.names = c("seqnames1", "start1", "end1", "strand1", "seqnames2", "start2", "end2", "strand2")
+#'     col.names = c(
+#'         "seqnames1", "start1", "end1", "strand1", 
+#'         "seqnames2", "start2", "end2", "strand2"
+#'     )
 #' ) |> as_ginteractions() 
 #' 
 #' gr <- GenomicRanges::GRanges(c("chr1:20-30:+", "chr2:55-65:+")) |>

R/arrange.R

@@ -16,7 +16,10 @@
 #' chr3 3 10 chr3 1 10
 #' chr4 4 10 chr4 1 10
 #' chr5 5 10 chr5 1 10",
-#' col.names = c("seqnames1", "start1", "end1", "seqnames2", "start2", "end2")) |> 
+#' col.names = c(
+#'   "seqnames1", "start1", "end1", 
+#'   "seqnames2", "start2", "end2")
+#' ) |> 
 #'   as_ginteractions() |> 
 #'   mutate(cis = seqnames1 == seqnames2, score = runif(5)*100, gc = runif(5))
 #' gi

R/count-overlaps.R

@@ -26,10 +26,15 @@
 #'     chr1 11 20 - chr1 51 55 + 
 #'     chr1 21 30 - chr1 51 55 + 
 #'     chr1 21 30 - chr2 51 60 +",  
-#'     col.names = c("seqnames1", "start1", "end1", "strand1", "seqnames2", "start2", "end2", "strand2")
+#'     col.names = c(
+#'         "seqnames1", "start1", "end1", "strand1", 
+#'         "seqnames2", "start2", "end2", "strand2"
+#'     )
 #' ) |> as_ginteractions() |> mutate(id = 1:4, type = 'gi')
 #' 
-#' gr <- GenomicRanges::GRanges(c("chr1:20-30:+", "chr2:55-65:-")) |> plyranges::mutate(id = 1:2, type = 'gr')
+#' gr <- GenomicRanges::GRanges(
+#'     c("chr1:20-30:+", "chr2:55-65:-")
+#' ) |> plyranges::mutate(id = 1:2, type = 'gr')
 #' 
 #' gi
 #' 

R/count.R

@@ -66,7 +66,9 @@
 #' @importFrom rlang expr
 #' @importFrom dplyr desc
 #' @export
-tally.GroupedGInteractions <- function(x, wt = NULL, sort = FALSE, name = NULL) {
+tally.GroupedGInteractions <- function(
+    x, wt = NULL, sort = FALSE, name = NULL
+) {
 
     ## Check provided name against gorup names
     name <- check_n_name(name, group_vars(x))

R/filter-overlaps.R

@@ -26,10 +26,14 @@
 #'     chr1 11 20 - chr1 51 55 + 
 #'     chr1 21 30 - chr1 51 55 + 
 #'     chr1 21 30 - chr2 51 60 +",  
-#'     col.names = c("seqnames1", "start1", "end1", "strand1", "seqnames2", "start2", "end2", "strand2")
+#'     col.names = c(
+#'         "seqnames1", "start1", "end1", "strand1", 
+#'         "seqnames2", "start2", "end2", "strand2")
 #' ) |> as_ginteractions() |> mutate(id = 1:4, type = 'gi')
 #' 
-#' gr <- GenomicRanges::GRanges(c("chr1:20-30:+", "chr2:55-65:-")) |> plyranges::mutate(id = 1:2, type = 'gr')
+#' gr <- GenomicRanges::GRanges(
+#'     c("chr1:20-30:+", "chr2:55-65:-")
+#' ) |> plyranges::mutate(id = 1:2, type = 'gr')
 #' 
 #' gi
 #' 

R/filter.R

@@ -18,7 +18,10 @@
 #' chr3 3 10 chr3 1 10
 #' chr4 4 10 chr4 1 10
 #' chr5 5 10 chr5 1 10",
-#' col.names = c("seqnames1", "start1", "end1", "seqnames2", "start2", "end2")) |> 
+#' col.names = c(
+#'     "seqnames1", "start1", "end1", 
+#'     "seqnames2", "start2", "end2")
+#' ) |> 
 #'   as_ginteractions() |> 
 #'   mutate(cis = seqnames1 == seqnames2, score = runif(5)*100, gc = runif(5))
 #' gi

R/find-overlaps.R

@@ -3,10 +3,11 @@
 #' @section Rationale:  
 #' 
 #' `find_overlaps()` will search for any overlap between `GInteractions` 
-#' in `x` and `GRanges` in `y`. It will return a `GInteractions` object of length 
-#' equal to the number of times `x` overlaps `y`. This `GInteractions` will 
-#' have additional metadata columns corresponding to the metadata from `y`. 
-#' `find_overlaps_directed()` takes the strandness of each object into account. 
+#' in `x` and `GRanges` in `y`. It will return a `GInteractions` 
+#' object of length equal to the number of times `x` overlaps `y`. 
+#' This `GInteractions` will have additional metadata columns 
+#' corresponding to the metadata from `y`. `find_overlaps_directed()` 
+#' takes the strandness of each object into account. 
 #' 
 #' @section Pinned `GInteractions`:  
 #' 
@@ -38,10 +39,15 @@
 #'     chr1 11 20 - chr1 51 55 + 
 #'     chr1 21 30 - chr1 51 55 + 
 #'     chr1 21 30 - chr2 51 60 +",  
-#'     col.names = c("seqnames1", "start1", "end1", "strand1", "seqnames2", "start2", "end2", "strand2")
+#'     col.names = c(
+#'         "seqnames1", "start1", "end1", "strand1", 
+#'         "seqnames2", "start2", "end2", "strand2"
+#'     )
 #' ) |> as_ginteractions() |> mutate(id = 1:4, type = 'gi')
 #' 
-#' gr <- GenomicRanges::GRanges(c("chr1:20-30:+", "chr2:55-65:-")) |> plyranges::mutate(id = 1:2, type = 'gr')
+#' gr <- GenomicRanges::GRanges(
+#'     c("chr1:20-30:+", "chr2:55-65:-")
+#' ) |> plyranges::mutate(id = 1:2, type = 'gr')
 #' 
 #' gi
 #' 
@@ -168,19 +174,25 @@ find_overlaps_directed.GInteractions <- function(
 
 }
 
-.mcols_overlaps_update <- function(left, right, suffix, return_data_frame = FALSE) {
+.mcols_overlaps_update <- function(
+    left, right, suffix, return_data_frame = FALSE
+) {
 
     left_names <- names(mcols(left))
     right_names <- names(mcols(right))
     common_name <- intersect(left_names, right_names)
     lname_inx <- left_names %in% common_name
     rname_inx <- right_names %in% common_name
     if (any(lname_inx)) {
-        names(mcols(left))[lname_inx] <- paste0(left_names[lname_inx], suffix[1])
+        names(mcols(left))[lname_inx] <- paste0(
+            left_names[lname_inx], suffix[1]
+        )
     }
 
     if (any(rname_inx)) {
-        names(mcols(right))[rname_inx] <- paste0(right_names[rname_inx], suffix[2])
+        names(mcols(right))[rname_inx] <- paste0(
+            right_names[rname_inx], suffix[2]
+        )
     }
 
     if (!is.null(mcols(left))) {

R/flank.R

@@ -51,7 +51,8 @@ NULL
 flank_downstream <- function(x, width) UseMethod("flank_downstream")
 #' @rdname plyranges-flank
 #' @export
-flank_downstream.Ranges <- function(x, width) plyranges::flank_downstream(x, width)
+flank_downstream.Ranges <- function(x, width) 
+    plyranges::flank_downstream(x, width)
 #' @rdname plyranges-flank
 #' @export
 flank_downstream.PinnedGInteractions <- function(x, width) {

R/ginteractions-construct.R

@@ -60,7 +60,9 @@
 #' pair2 chr1 50000 chr1 70000 + +
 #' pair3 chr1 60000 chr2 10000 + +
 #' pair4 chr1 30000 chr3 40000 + -", 
-#' col.names = c("pairID", "chr1", "pos1", "chr2", "pos2", "strand1", "strand2"))
+#' col.names = c(
+#'   "pairID", "chr1", "pos1", "chr2", "pos2", "strand1", "strand2")
+#' )
 #' pairs |> 
 #'   as_ginteractions(
 #'     seqnames1 = chr1, start1 = pos1, width1 = 1000, 
@@ -84,7 +86,9 @@
 #' chr1 1000 5000 chr1 3000 3800",
 #' col.names = c("chr1", "start1", "end1", "chr2", "start2", "end2"))
 #' df |> 
-#'   as_ginteractions(seqnames1 = chr1, seqnames2 = chr2, strand1 = '+', strand2 = '-')
+#'   as_ginteractions(
+#'     seqnames1 = chr1, seqnames2 = chr2, strand1 = '+', strand2 = '-'
+#'   )
 #' 
 #' data.frame(type = "cis", count = 3) |> 
 #'   as_ginteractions(
@@ -150,7 +154,9 @@ as_ginteractions.data.frame <- function(
     # Look for end*/width* fields
     for (name in c('end1', 'end2')) {
         if (!(any(name %in% c(names(rd), names(.data))))) {
-            if (!(any(gsub("end", "width", name) %in% c(names(rd), names(.data))))) {
+            if (!(any(
+                    gsub("end", "width", name) %in% c(names(rd), names(.data))
+                ))) {
                 stop(
                     "Please provide end/width information.", 
                     call. = FALSE
@@ -184,15 +190,18 @@ as_ginteractions.data.frame <- function(
     gi
 }
 
-.gi_construct <- function(.data, rd, col_names, core_gi, starts.in.df.are.0based) {
+.gi_construct <- function(
+    .data, rd, col_names, core_gi, starts.in.df.are.0based
+) {
 
     ## Check that all required columns are found, either in .data or ...
     match_cols_i <- names(core_gi) %in% col_names
     match_quosures_i <- names(core_gi) %in% names(rd)
     if (sum(c(match_cols_i, match_quosures_i)) < 8) {
         stop("Unable to construct GInteractions from .data. 
             Specify the column name used for each required field: 
-            seqnames1, start1, end/wdith1, strand1, seqnames2, start2, end/wdith2, strand2",
+            seqnames1, start1, end/wdith1, strand1, 
+            seqnames2, start2, end/wdith2, strand2",
                 call. = FALSE)
     }
 

R/ginteractions-env.R

@@ -48,7 +48,9 @@ setMethod("as.env", "GInteractions", function(x, enclos, tform = identity) {
     env <- S4Vectors::as.env(
         x@delegate, 
         envir, 
-        tform = function(col) unname(S4Vectors::splitAsList(col, x@group_indices))
+        tform = function(col) unname(
+            S4Vectors::splitAsList(col, x@group_indices)
+        )
     )
     rlang::new_data_mask(env, top = parent.env(env))
 }