Ran github actions

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: transmogR
 Type: Package
 Title: Modify a set of reference sequences using a set of variants
-Version: 0.99.1
+Version: 0.99.2
 Authors@R: person("Stevie", "Pederson", 
     email = "stephen.pederson.au@gmail.com", 
     role = c("aut", "cre"),
@@ -22,11 +22,9 @@ Depends:
     GenomicRanges
 Imports:
     BSgenome,
-    ComplexUpset,
     GenomeInfoDb,
     GenomicFeatures,
     ggplot2,
-    InteractionSet,
     IRanges,
     methods,
     parallel,
@@ -39,7 +37,9 @@ Imports:
 Suggests:
     BiocStyle,
     BSgenome.Hsapiens.UCSC.hg38,
+    ComplexUpset,
     extraChIPs,
+    InteractionSet,
     knitr,
     rmarkdown,
     rtracklayer,

NAMESPACE

@@ -22,9 +22,6 @@ importClassesFrom(VariantAnnotation,VcfFile)
 importFrom(BSgenome,getSeq)
 importFrom(Biostrings,IUPAC_CODE_MAP)
 importFrom(Biostrings,getSeq)
-importFrom(ComplexUpset,intersection_size)
-importFrom(ComplexUpset,upset)
-importFrom(ComplexUpset,upset_set_size)
 importFrom(GenomeInfoDb,"genome<-")
 importFrom(GenomeInfoDb,"seqinfo<-")
 importFrom(GenomeInfoDb,"seqlevels<-")
@@ -41,7 +38,6 @@ importFrom(IRanges,overlapsAny)
 importFrom(IRanges,start)
 importFrom(IRanges,subsetByOverlaps)
 importFrom(IRanges,width)
-importFrom(InteractionSet,GInteractions)
 importFrom(S4Vectors,"mcols<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,mcols)

R/genomogrify.R

@@ -61,7 +61,7 @@ setMethod(
     "genomogrify",
     signature = signature(x = "XStringSet", var = "GRanges"),
     function(
-        x, var, alt_col = "ALT", mask, tag = NULL, sep = "_",
+        x, var, alt_col = "ALT", mask = GRanges(), tag = NULL, sep = "_",
         var_tags = FALSE, var_sep = "_", verbose = TRUE, ...
     ) {
 
@@ -72,9 +72,7 @@ setMethod(
         ## 5. Optionally tag sequence names
         ##    - Use a common tag + specific tags for SNPs/Insertions/Deletions
 
-        if (missing(mask)) mask <- GRanges()
         stopifnot(is(mask, "GRanges"))
-
         ## Check the variants are valid
         var <- .checkAlts(var, alt_col)
         var <- var[!overlapsAny(var, mask)]
@@ -129,7 +127,7 @@ setMethod(
     "genomogrify",
     signature = signature(x = "BSgenome", var = "GRanges"),
     function(
-        x, var, alt_col = "ALT", mask, names, tag = NULL, sep = "_",
+        x, var, alt_col = "ALT", mask = GRanges(), names, tag = NULL, sep = "_",
         var_tags = FALSE, var_sep = "_", verbose = TRUE, ...
     ) {
         ## Setup the sequence info
@@ -153,7 +151,7 @@ setMethod(
     "genomogrify",
     signature = signature(x = "BSgenome", var = "VcfFile"),
     function(
-        x, var, alt_col = "ALT", mask, names, tag = NULL, sep = "_",
+        x, var, alt_col = "ALT", mask = GRanges(), names, tag = NULL, sep = "_",
         var_tags = FALSE, var_sep = "_", which, verbose = TRUE, ...
     ) {
         var <- .parseVariants(var, alt_col, which)
@@ -171,7 +169,7 @@ setMethod(
     "genomogrify",
     signature = signature(x = "XStringSet", var = "VcfFile"),
     function(
-        x, var, alt_col = "ALT", mask, tag = NULL, sep = "_",
+        x, var, alt_col = "ALT", mask = GRanges(), tag = NULL, sep = "_",
         var_tags = FALSE, var_sep = "_", which, verbose = TRUE, ...
     ) {
         var <- .parseVariants(var, alt_col, which)

R/helpers.R

@@ -50,10 +50,9 @@
 }
 
 #' @keywords internal
-#' @importFrom ComplexUpset intersection_size
 .makeIntersectionArgs <- function(x){
     stopifnot(is(x, "list"))
-    args <- as.list(formals(intersection_size))
+    args <- as.list(formals(ComplexUpset::intersection_size))
     args <- args[names(args) != "..."]
     cmn <- intersect(names(x), names(args))
     novel <- setdiff(names(x), names(args))
@@ -63,10 +62,12 @@
 }
 
 #' @importFrom S4Vectors mcols mcols<-
-#' @importFrom InteractionSet GInteractions
 #' @keywords internal
 .giFromSj <- function(sj, tx_col, rank_col) {
 
+    if (!requireNamespace('InteractionSet', quietly = TRUE))
+        stop("Please install 'InteractionSet' to return a GInteractions object.")
+
     stopifnot("site" %in% colnames(mcols(sj)))
     stopifnot(all(sj$site %in% c("donor", "acceptor")))
     stopifnot(is.numeric(mcols(sj)[[rank_col]]))
@@ -85,7 +86,7 @@
     if (any(is.na(dnr_to_acc))) stop("NA values when mapping junctions")
 
     cols <- setdiff(colnames(mcols(dnr)), c("site", rank_col))
-    gi <- GInteractions(
+    gi <- InteractionSet::GInteractions(
         anchor1 = granges(dnr)[dnr_to_acc],
         anchor2 = granges(acc)[acc_to_dnr]
     )

R/indelcator.R

@@ -71,9 +71,6 @@ setMethod(
     signature = signature(x = "XString", indels = "GRanges"),
     function(x, indels, exons, alt_col = "ALT", ...) {
 
-        ## Check classes (Not needed for S4)
-        cl <- class((x))
-
         ## Get the variants matching the exons
         indels <- subsetByOverlaps(indels, exons)
         strand(indels) <- "*"
@@ -118,6 +115,7 @@ setMethod(
         df$alt <- df$seq
         alt <- mcols(indels)[[alt_col]]
         names(alt) <- indels$ID
+        cl <- class((x)) # Needed for coercion at the final step
         if (neg_stranded) {
             new_cl <- paste0(cl, "Set")
             alt <- as.character(reverseComplement(as(alt, new_cl)))

R/owl.R

@@ -54,7 +54,6 @@ setMethod(
     function(seq, snps, alt_col = "ALT", ...) {
 
         ## Check the SNPs
-        stopifnot(is(snps, "GenomicRanges"))
         snps <- .checkAlts(snps, alt_col)
         stopifnot(all(width(snps) == 1)) # Must be single positions
         stopifnot(all(nchar(mcols(snps)[[alt_col]]) == 1)) # Must be SNPs

R/upsetVarByCol.R

@@ -43,7 +43,6 @@
 #'
 #' @importFrom S4Vectors splitAsList mcols
 #' @importFrom IRanges subsetByOverlaps
-#' @importFrom ComplexUpset intersection_size upset_set_size upset
 #' @importFrom ggplot2 aes geom_bar geom_text after_stat ggtitle position_stack
 #' @importFrom ggplot2 scale_y_reverse scale_y_continuous expansion ylab
 #' @importFrom rlang list2 :=
@@ -55,6 +54,9 @@ upsetVarByCol <- function(
         hjust_counts = 1.1, set_lab = "Set Size", title
 ){
 
+    if (!requireNamespace('ComplexUpset', quietly = TRUE))
+        stop("Please install 'ComplexUpset' to use this function.")
+
     stopifnot(is(gr, "GRanges"))
     mcol <- match.arg(mcol, colnames(mcols(gr)))
 
@@ -79,11 +81,11 @@ upsetVarByCol <- function(
     df_list <- list(ids = ol_ids, lapply(ol, \(x) ol_ids %in% x))
     df <- as.data.frame(df_list)
     base_args <- .makeIntersectionArgs(intersection_args)
-    base_ann <- do.call("intersection_size", base_args) +
+    base_ann <- do.call(ComplexUpset::intersection_size, base_args) +
         scale_y_continuous(expand = expansion(c(0, 0.05)))
     if (is.character(title)) base_ann <- base_ann + ggtitle(title)
 
-    sets <- upset_set_size(geom = set_geom) + ylab(set_lab) +
+    sets <- ComplexUpset::upset_set_size(geom = set_geom) + ylab(set_lab) +
         scale_y_reverse(expand = expansion(c(set_expand, 0)))
     if (set_counts) {
         count <- c()
@@ -92,7 +94,7 @@ upsetVarByCol <- function(
         )
     }
 
-    upset(
+    ComplexUpset::upset(
         df, names(var_list),
         base_annotations = list2("{intersection_lab}" := base_ann),
         set_sizes = sets, ...

vignettes/creating_a_new_reference.Rmd

@@ -53,10 +53,7 @@ require installation.
 ```r 
 if (!"BiocManager" %in% rownames(installed.packages()))
   install.packages("BiocManager")
-pkg <- c(
-  "rtracklayer", "BSgenome.Hsapiens.UCSC.hg38", "extraChIPs", "transmogR"
-)
-BiocManager::install(pkg, update = FALSE)
+BiocManager::install("transmogR")
 ```
 
 Once these packages are installed, we can load them easily